Answers to 18 Payroll Questions You Are Dying to Ask

For some business owners, running payroll might be like learning a foreign language. You are a master of your business idea, not the administrative responsibilities that come with it. Because you might not be familiar with these responsibilities, you might have some payroll questions.

Payroll questions and answers

When you become an employer, you need to run payroll for your employees. You need to handle everything from setting up payroll to maintaining records. Ask all the payroll-related questions you can think of to stay organized and legal. Otherwise, you could end up with disgruntled employees, penalties, or fines.

Here are some common payroll questions that might help you in your small business. They are organized by category.

Questions to ask when implementing a new payroll system

Becoming a new employer is a process. For many startup business owners, hiring new employees can be stressful. Here are some payroll questions to ask when getting started as an employer.

1. What is an EIN?

EIN stands for Employer Identification Number. The IRS assigns you an EIN so you can identify your business on different tax documents. Like a Social Security number, an EIN is a taxpayer identification number. When you become an employer, you need to apply for an EIN. You can obtain an EIN by applying online or faxing/mailing Form SS-4 to the IRS.

Need to know all of the accounts to register for before hiring?

Download our FREE whitepaper, Hiring Employees Guide & Checklist, for accounts to register for, hiring information, a handy checklist, and more.

2. What payroll terms do I need to know?

There are many terms associated with running payroll. Here are a few payroll terms you should familiarize yourself with:

  • Compensation: Everything you give employees in exchange for their work, like wages, bonuses, and small business employee benefits.
  • Deduction: The money you withhold from an employee’s wages for taxes, benefits, etc.
  • Gross wages: An employee’s wages before deductions.
  • Net wages: An employee’s wages after deductions are taken out.

3. What’s the best way to run payroll?

There are a few ways you can run payroll, depending on what you feel most comfortable with. Business owners can outsource their payroll to a specialist, run payroll by hand, or use payroll software. Generally, outsourcing payroll to a payroll accountant or PEO (professional employer organization) is the most expensive and least time-consuming method while learning how to do payroll by hand is the least expensive and most time consuming. Using payroll software can be a good middle ground to save yourself time and money.

Interested in running payroll on your own but want a reliable solution to back you up? Give Patriot’s online payroll software a free try!

Questions about paying employees

The point of running payroll is so employees get their correct wages and the government gets its money, too. Here are some questions you might have about the process of actually paying your employees.

4. Is direct deposit a good way to pay employees?

When it comes to how to pay employees, direct deposit is one payment type you can offer employees. Many business owners like direct deposit because it is convenient. You can pay employees without having to hand them a physical check, which also makes it a safe payment option. You don’t need to worry about employees losing paychecks with sensitive business information. Some states let employers implement mandatory direct deposit.

5. Am I allowed to pay employees in cash?

Yes, it is legal to pay employees in cash. But, you might come under more scrutiny if you do. Paying employees in cash is often associated with avoiding taxes. If you decide to pay employees in cash, remember to take out taxes and deductions before giving employees their final take-home pay. And, keep accurate records in case you do come under the IRS’s watch.

6. What is a pay stub?

A pay stub lists details about an employee’s paycheck, including their gross wages, taxes and other deduction amounts, and the employee’s take home, or net, pay. The pay stub also includes information like the pay period and date. Some states require that you provide either a physical or electronic pay stub for each payroll you run.

Questions about additional pay

Sometimes, regular wages aren’t the only payments you’ll give to employees. See what else you need to know about additional payments.

7. What is supplemental pay?

Supplemental wages are dollars you give employees in addition to regular wages. A few examples of supplemental wages are bonus payments, commissions, and severance pay. Because supplemental pay is not part of an employee’s regular wages, you withhold taxes differently from them. You can choose between the percentage and aggregate methods. With the percentage method, you must withhold a flat rate of 25% on the employee’s supplemental wages. With the aggregate method, you must add the employee’s supplemental wages to their regular wages and withhold tax from the updated tax bracket.

8. What is overtime?

Understanding the Fair Labor Standards Act’s (FLSA’s) laws on overtime is essential. Overtime is any time worked beyond 40 hours in a workweek. If a nonexempt employee puts in overtime hours, you must pay overtime wages. Overtime wages are one and one-half times the employee’s hourly wages for hours worked over 40 each workweek. For example, if an employee earns $16 per hour and works three hours of overtime, they would earn a total of $72 in overtime wages ($16 X 1.5 X 3).

9. What is the difference between an exempt and nonexempt employee?

Unless an employee is exempt, you must pay them overtime wages. Exempt employees must meet one of the following types of exemption:

  1. Executive, administrative, or professional exemption
    • Earns a salary,
    • Makes at least $35,568 per year ($684 per week), AND
    • Has high-level job responsibilities that qualify for exemption (i.e., executive, administrative, or professional duties)
  2. Computer exemption
    • Receive a salary of at least $684 per week or a fee of at least $27.63 per hour,
    • Work as a computer system analyst, computer programmer, software engineer, or something similar, AND
    • Have primary duties that meet the FLSA’s computer exemption requirements
  3. Outside sales exemption
    • Has a primary duty of making sales or obtaining orders or contracts AND
    • Is regularly engaged away from the main business office
  4. Highly compensated employee exemption
    • Receive annual compensation totaling $107,432 or more
    • Perform at least one of the executive, administrative, or professional duties

If the employee does not meet the above requirements, they are nonexempt. In that case, you must pay them at least the federal minimum wage and overtime wages.

Questions about taxes

Taxes are an inevitable part of running a business and paying employees. Here are some questions you might ask about taxes.

10. What taxes do I need to withhold from an employee’s paycheck?

You must withhold federal income, Social Security, and Medicare taxes. You might also need to withhold state and local income taxes depending on your locality. Federal income tax is determined by an employee’s Form W-4 and the tax brackets found in Publication 15. Social Security and Medicare taxes make up FICA tax. FICA tax is 7.65% of an employee’s pay. You also need to make a matching employer contribution of 7.65% for each of your employees. Withhold Social Security tax until you reach the Social Security wage base. There is no wage base for Medicare; there is an additional Medicare tax, however.

Only withhold taxes from employees, not independent contractors. Our free whitepaper, A Guide to Independent Contractors vs. Employees can help.

12. What taxes do I need to deduct from my income?

As an employer, you are not off the hook when it comes to taxes. But, how you pay taxes depends on your business structure. If you are incorporated and receive a salary, payroll and income taxes are deducted from your gross wages. If you are self-employed, you do not receive a salary, but you still need to pay taxes on your income. Instead of FICA tax, you must pay self-employment tax. With self-employment tax, you pay the entire 15.3% for Social Security and Medicare taxes. And, you need to pay income tax. Self-employed individuals pay estimated taxes, which includes both self-employment and income taxes.

11. What is unemployment tax?

There are federal and state unemployment taxes. When you have employees, you are responsible for paying FUTA (Federal Unemployment Tax Act) tax and SUTA tax (state unemployment). Generally, you do not withhold unemployment tax from an employee’s wages. The FUTA tax rate is 6%, but most employers only pay 0.6% due to a tax credit. You only pay FUTA tax on the first $7,000 each employee earns. Your state determines your SUTA tax rate. When you hire your first employee, you must register with your state unemployment agency. They will let you know your SUTA tax rate.

Questions about benefits

Offering benefits is a great way to attract and keep employees. Here are some questions you might have about benefits.

13. What is the difference between an FSA and HSA?

FSAs (flexible spending accounts) and HSAs (health savings accounts) are great benefits you can offer employees. While both are healthcare plans that reduce an employee’s income tax liability, you need to understand the difference between FSA vs. HSA. Employees can contribute up to $2,650 per year to their FSAs and $3,450 for self-only coverage / $6,900 for family coverage to their HSAs in 2018. There are other differences, including ownership, eligibility to contribute, access to money, rollover rules, and more.

14. What are fringe benefits?

Benefits are an important part of an employee’s full compensation package. Fringe benefits include health insurance, educational assistance, and stock options. Fringe benefits can be taxable or nontaxable. Nontaxable fringe benefits are not subject to federal income tax withholding, FICA tax, or FUTA tax. The IRS determines the taxes that apply to different types of fringe benefits.

15. What are pre-tax deductions?

Pre-tax deductions are amounts you take out of an employee’s gross wages before withholding taxes. This lowers the employee’s taxable income, which can save them more money. Some pre-tax deductions include retirement plans, health insurance, FSAs, and HSAs.

Payroll FAQ about forms and recordkeeping

Here are some questions you might have about filing forms and keeping documents for your records.

16. What forms do employees need to know about?

All employees are required to fill out Form W-4, Employee’s Withholding Allowance Certificate, and Form I-9, Employment Eligibility Verification, before they can start working at a business. Use Form W-4 to determine how much to withhold from an employee’s wages for federal income tax. Use Form I-9 to verify that an employee is legally allowed to work in the United States. Employees might also need to fill out state tax withholding forms, benefits forms, and more.

17. Which forms do I need to know about?

Filing forms needs to become second nature when you run a business. The most common forms you should keep track of include:

  • Form W-2, Wage and Tax Statement: Create a form for each employee you paid wages to. Send a copy of this form to the Social Security Administration; state, city, or local tax departments (if required); and to the employee by January 31. You also need to keep a copy for your records.
  • Form W-3, Transmittal of Wage and Tax Statements: This is a form that summarizes your Forms W-2. Send Form W-3 to the Social Security Administration along with Forms W-2 by January 31.
  • Form 940, Employer’s Annual Federal Unemployment: File this form annually to report your FUTA tax payments.
  • Form 941, Employer’s Quarterly Federal Tax Return: Report federal income and payroll taxes on this form quarterly OR
  • Form 944, Employer’s Annual Federal Tax Return: An alternate to Form 941, file this once a year to report federal income and payroll taxes. You can only use this form if the IRS notifies you.

18. How long do I need to keep payroll records?

Hanging onto records is also part of being a small business employer. You need to keep all payroll records for at least three years, according to the FLSA. And, you must keep all records of employment taxes for at least four years after filing the fourth quarter of the year, according to the IRS. Basically, your payroll record retention should last for a long, long time.

Need help simplifying payroll? Patriot Software’s Full Service Payroll has you covered. Our payroll services let you run payroll with our three-step process, handle your tax obligations for you, and more. Try us for free!

This article has been updated from its original publication date of March 5, 2018.

This is not intended as legal advice; for more information, please click here.

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