Hi there crystalst,
It's important that all your payroll information is entered correctly for your employees to get paid the right amount. QuickBooks Online Payroll is a great tool able to help you calculate and pay your employees based on the hours they've worked for your company. I can point you in the right direction for assistance with payroll not affecting your books correctly.
If your pay is no longer affecting your books correctly. I recommend reaching out to the QuickBooks Online Payroll support team outside of the community. They'll be able to view how your payroll is set up in the system, your projects as well as some pay runs to see what's going on with your pay affecting the books and projects differently. You can reach out to them using these steps:
Schedule a Callback or start a Chat: click (?)Help in the upper right > type and enter "Contact support" into the QB Assistant > click Contact Us > explain your situation > click Let's Talk > choose Get a callback or Start a Chat.
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If you have any other questions, feel free to reach out here.
