Here is how I do it:
I set up a Bank Type account in QB and name it Payroll Clearing. The Net Paychecks that will be EFT (ACH) are "From" this account. Now payroll clearing is Negative a total.
In my bank's ACH site, I create a recurring Template listing everyone participating with their routing and account info. I log in and update the values with the current Takehome pay and initiate. This is the same total = I made no typos.
In QB, that Total is an entry as a Transfer, from Real Checking to Payroll Clearing. This matches the statement activity for Real Checking and Payroll Clearing = 0.