paying vendors

I am new to QuickBooks Premier for Contractors, and I am having a problem adding back charges onto the paychecks. I don't use the payroll program, the company just has me "enter a bill" from the subcontractor, then I go to "pay bills". Is there anyway to do a back charge, and have it show up on the check stub so the subcontractor can see why his pay is less than expected? Any help would be greatly appreciated! Thank you in advance for anything. Abby