Same way you know your power company counts your use properly. Or the water company. You just trust that they do it.

Someone like CCBill would have no incentive to fudge your stats since they get a cut of the sale before you get yours and they do the tracking. As for programs using 3rd party tracking software, research to see if someone raised an issue with payouts or missing sales, give them a try and don't put your eggs all in one basket