The commission rules are set in the apptly named Commission Rules screen, which can be found in the Go To menu under Manufacturers Reps.
The simplest form of a commission rule is shown in this image. This rule will apply a 10% commission to all invoice or line items imported for Jackson Manufacturing. If you need to be more specific of a particular customer (someone gets a different rate, like a large national distributor) or a particular product (we are paid more on the machine line then the renewables, for example), enter a rule for each different case.
Make sure to always review results of an invoice import to make sure the totals sales and commission match what you were expecting.