Should the cost of customizing our product be deducted from sales credit?

Regarding the cost of customization, now you are talking about paying on the margin of the deal, not the revenue value. That's fine too - but would probably result in a higher commission rate. If you can accurately predict the margin value of the deal, it is an even better measure of the value created by the sales person. Many companies avoid this, however, because it results in hair-raising accounting at a contract level and lot of discussion and argument that can actually cut into your sales capacity. But if you can do this in a straight forward way, it is a great way to measure sales people.