Don't put anything on it until you treat it and stop the corrosion and electrolysis. Bare aluminum will react with a lot of things. If you cover it, the corrosion will continue under the cover. This happens in the airline industry and with the marine industry. You will need to get your boat off of the trailer, up on jacks, then use the acid cleaner first on all of the spots, wash off, then use Alodine, the converter, and leave it on until the metal turns yellow (not too long or it turns orange or brown), then you can paint with a two part epoxy paint used to paint aluminum boats. You could also paint with clear coat Polyurethane just to cover it and protect your conversion. Yes, the metal is thinner, but after treating and painting you should be ok. Since the aluminum is converted now you could paint then apply the filler and repaint, but don't know if all that would adhere properly. Note; you have to paint over the converted yellow aluminum to protect it or it will scratch off on mud or oysters or sand and start the corrosion all over. I had it on my Boatright from carpet and replaced the carpet with plastic bunks. I got my chemicals from Crest Chemicals off of 288. One is the Acid cleaner12 (like Alumaprep) and the converter is PCC6, the same as Alodine. Their number is 800-622-9006. Ask to talk to Doug, the sales manager. He will tell you how to apply too. It is not hard to do but it is acid so wear goggles and gloves and long sleeves. You have to do it right. This was told to me by my aluminum welder who repairs this stuff all the time. If push comes to shove and you get a spot that is too thin he said he can patch it but it is not cheap. Gotta stop the electrolysis and corrosion first though still. You can PM me if needed.