I've done both. I think it is better to do it before, but if you are using chalk or a pouncer you have to do it after it is sandwiched. I say to do it before, but I seem to be much like everyone else--I forget to, or don't have the right marking thing, or haven't figured out what to do. Most often I just free motion quilt everything. I have found if you figure out what you want to free motion in the different blocks of the quilt, practice on paper and when you are ready to quilt it is second nature.