"do you use an upload to payroll or manual entry?"

QB Desktop has Payroll functions in it. You can pay for the tax table subscription or "run manually" in the QB US as long as you never enabled Multi-Currency.

"Client has about 50 checks with majority holding overtime."

That's Banking. That isn't Payroll, but Takehome and Tax payments.

"They utilize a time tracking system that exports to QBs."

That's Tasks. That isn't Cost data. Costs come from Paying for something.

For instance, in Desktop, you use the timesheet, you set the Preferences to Job Track Per Earnings item, so that you can Reiterate the pay item, and you set the Employee Default to Pay From Time Data, so that the single activity view or weekly view for task entries includes both the Payroll Item and the Service item, for job tracked task lines. Now, when you Run Payroll, that info is passed to the paycheck, giving Job Cost allocations, including Employer taxes. The Payroll item flows the pay data to the accounting, the Service item links that cost to the Service for Job tracking, and now you have all the reporting, including quantity, and the ability to compare estimates to actuals by quantity and/or values, to compare revenue to cost for that same service, if that is something you sell, etc.

Please see my attachment.