Set up who the reps are, then the rules: a percentage of the sale, of the margin, or a fixed amount, optionally limited to a customer or a kind of work.
Commission is earned when the sale happens and calculated on its own. By rep shows what each person has earned for a period.
Nothing is paid until somebody presses Approve. A rule that pays automatically is a rule that pays on an invoice that is later voided.
Deleting a rule
Commissions already earned are kept. Changing how you pay in future should not rewrite what somebody was already promised.