The best way I have found to get a report that shows net profits to pay out commission is to run the following report:

Go to Reports, then go to Company & Financial, then go to Income by Customer Summary....

The filters absolutely do not work at all, but at least I can see the net profits by customer. I will have to export the file to Excel and filter by sales rep that way manually.  This report also allows you to drill down into each customer so you can print each one separately if needed.