If your using an external payroll service then you can choose how much information detail you want to enter in QB. This decision effects how the entries must be made.
If you just want 'payroll summary' info in QB then you will enter based on the summary report from the service. If you want to see within QB how much was paid individually then you will be entering based on the individual paystubs.
In either method I will suggest you use a 'payroll service clearing account' to process the entries thru - this can be a dummy manual bank account. The 2 bank withdrawls go into the clearing account, and then the disbursements made by the payroll service are posted, in either detail or summary form.
The 2 step withdrawl that your service does is odd, but doesn't really change anything.