Commonly, the soft side goes on the board, and the hook side goes on the pedals.
Personally, I remove rubber feet. If they have screws in them holding the pedal together, just screw the screw back in without the rubber foot. Velcro will stick much better on pedals like Boss ones if you remove the rubber backing, yes. Although I think with Boss ones, you MIGHT be able to just flip the back plate round and still have it all screw back together if you don't want to remove the rubber. Don't quote me on that though.