Hi Thomas,
QuickBooks offers a powerful Projects feature which is designed to save you time. I'd be glad to steer you in the right direction with figuring out why the Projects feature is accounting for payroll costs twice.
Based on what you've described, I can see how the payroll costs are being accounted for twice. Since your employees are getting paid using the Payroll Timesheets, do you still need to add hours again to their payroll when you run it each month?
In order to get to the bottom if this ASAP, it's important I see how your account is set up so I can instruct on what the next best steps would be. I recommend contacting our support team using this link here. In the meantime, I also recommend checking out this helpful article: How to turn on and set up time tracking.
Let me know if you have other questions by leaving a comment below. I'll be on standby.