If you ran payroll in QuickBooks, all of the transactions should be categorized already and entered into the General Ledger, broken out between salaries/wages, taxes, and other payroll items (benefits, reimbursements, etc.)
If you are using the banking import function, you just need to remove those Net Pay transactions from the list, otherwise they will be double entered. (Again, this all assumes payroll was ran in the QuickBooks file).
If payroll was NOT run through QuickBooks and you are entering payroll, the Net Pay probably needs to be entered as a journal entry with a debit to gross Wages/Salary expense and a credit to the deductions to arrive at net pay (taxes, retirement deferrals, etc.)
I hope I'm understanding the question correctly.
