I am anal about my finances in general so I use quicken. Even though it is a bloated piece of crap it is still the best way to keep good records and track how much you are actually making from these activities. I have separate accounts for each re-loadable card so when I buy a reload the CC transaction shows as a transfer to that card's account and an expense category for the associated fees. From this I can run a quick report to see how much I am really making. It helps that I am earning cash and not miles but if you were earning miles you would just create an entry where the cost of a ticket used was entered as cash back received.

I also use the mobile app to snap a picture of each receipt so the receipt is attached in quicken to the transaction should a problem arise.

On the physical side I have two expanding files where I store each type of churn source and receipt. Each month I discard the cards from the month before so this weekend I will empty the December folder and start filling it with February. That way I have the physical receipt and card for a minimum of 30 days which is more than enough time to find out if there is a problem.