Hi there Mina, 

It's awesome that you've started to use the Timesheets feature with your QuickBooks Desktop Payroll in order to help calculate job costing easier. Knowing how much money is spent on certain projects is a key part of running your business. I can provide some insight into this matter.

Job costing in QuickBooks Desktop is calculated based on the hours in the timesheet and not the ones in payroll. If you've made timesheets for 90 hours' worth of work, then while running payroll you adjust it to 80 hours, it'll appear as 80 hours on the paycheque, but will remain 90 in your timecard. Since the data for the job cost will be based on the timesheet, it'll be calculated based on 90 hours. You can verify this by going to check your Timesheet that you originally created to make sure it is unchanged, or by running a job report like the Time by Job Summary or Time by Job Detail. To access these reports, you'd click on Reports in the top bar, then select Report Centre. You'll find them in the category named Jobs, Time & Mileage located in the left column.  Here's an article I find useful regarding the use of Job Costing In QuickBooks Desktop. You can find some more articles like these in your QuickBooks Desktop account by following these steps:

• Select the Help menu from the top menu bar.
• Choose QuickBooks Desktop Help.
• Select the Help tab, then click Search.
• Use keywords like "timesheets" or "job costing" to find related articles
• Click an article to learn more.

I hope this helps clarify how Job Costing is affected by salaried employees. Have a great day.