You should have run it prior to flashing the new rom to backup your apps. Then flash rom and run it again to clean, then once more to flash the additional scripts to get the full RC effect . But just running the cleaner after the rom is fine too
It moves them to internal storage, after you restore them they will be deleted automatically so it frees the space back up. Yes I've seen that but Rom Cleaner does all that for me, thanks tho!
actually theres plenty on that list that RC doesn't do...