Hi Todd,
I had the same problem with my timing belt - slapping the cover. I think I might have fixed it by loosening the cam sprockets while I set the timing belt tension. I think I've seen a few other posts on the forum, though, that say the belt hitting the cover is a constant problem regardless of the belt tension. Who knows... Maybe you'll get lucky and the new belt won't be a problem. Replacing the top section of the cover, after the fact, shouldn't be too tough if the belt still slaps the cover.
Good luck,
Josh