paradocs,
Good question. In order not to get confused with which card is registered with which program, I wrote the list down on a sheet of paper. Eventually, I memorized which card is registered with which airline program.
In general, I don't dine out a lot in restaurants that belong to the programs. Howevever, I frequenlty would check to see which restaurants in the vicinity of my neighborhood participate in the programs. I now more or less have memorized which ones they are. When I do dine out in these restaurants, I would use my credit card of choice to earn miles, my Amex Sheraton Starwood card. I registered this with the frequent flier program that I enjoy earning the most miles.
I would keep the dining receipts in a separate envelope. I do check the airline's website to see whether or not my miles for a certain dining experience have posted. Once I see that they have, I would throw the receipts away. (BTW, all the miles have posted. I have never been cheated out of a single mile.)
In general, my recommendation is to try to use a primary card for your dining mileage earning opportunities. Only when you realize that you have eaten at a particluar restaurant previously in the month should you resort to using your secondary card(s). If you want, you may want to initiate a record keeping of your dining acitivities on to monitor your monthly mileage earning progress.
I tend to remember which ones I have been to in a month. If I see that I am revisiting that restaurant, I just remind myself to use my secondary cards.
I hope this answered your question somewhat.