My can of Interdeck non-skid paint says to wash down fiberglass decks with soap & water using a stiff brush. Rinse & let dry, then sand with 180-220 sandpaper, After that, paint.
If the deck was previously painted they call for finer sandpaper, followed by a wipedown with their brushing liquid, to pick up paint residues. Keeping THAT off the topsides might be an issue, as you suggest. If your deck isn't painted, this shouldn't be a problem.