Best practice for paying Commission Bills using external payroll

(I'm an accounting newbie, please be gentle)

We use the commission module to calculate commissions for inside sales staff as well as outside contractors. As you know, when a commission is authorized it creates a Bill to be paid.  We run all payroll through an outside 3rd party.  According to my accountant he then writes a "pseudo check" (Check w/out printing a check) to the payroll company and links it to our labor accounts.

So this has worked fine except we've had these commission bill records piling up and throwing off everything.  So I guess actually it hasn't been working fine