All I can tell you is what I do with my Thermarest. I fold it in half, lengthwise, then I roll it, secure it so it won't unroll, and put it inside my pack. This approach causes me no problems, so I continue to do it this way.

Whenever I make a fairly significant change to my gear setup, there follows a period of experimenting with how best to pack my pack. It usually settles in to a routine rather quiickly, but the best test of a packing solution is experiencing it on the trail for a few days.