Let's go ahead and isolate why it's not calculating the federal taxes, Bjones317.
Our program calculates the tax based on these factors:
Number of allowances/dependents
Then, these are the possible reasons why it's not taking out the taxes:
Annualized salary exceeds the salary limit
The gross wage of the employees are too low
Let's try to manually calculate the employee's paycheck, then verify if it matches with QuickBooks Online. To help us compute the exact withholding amount, go through the IRS 2018 Publication 15, and use the Percentage method (page 44-45). This is the same method used by QBO to calculate the federal taxes.
You can tag me if you need more help. I'll help you in any way I can.