I’m pretty sure that I’m getting leaks from my rub rail. I get water coming into the engine bay on identical sides at the joint in the hull and in my cuddy. I’ve decided against sealing the leaking spots in the engine bay, I think that’s the design to indicate bad rub rail seals? Is it? Should I pull the rub tail off and check under it? The rub rail needs to be re-caulked regardless so what’s the best method, slow steady hand and 3m marine silicone caulking?

looking at pics, it shouldnt be underwater..... And do not use 5200. I dont care what your mom's boyfriend's cousin's buddy tells you, do not use 5200. You want a sealant not an adhesive. you are not permanently attaching the rubrail and screws.

The proper way to do it is to remove the rubrail and then seal the joint between the hull and deck.
You can use 3M 5200 for that and it will strengthen the joint as well.
When you reinstall rubrail, put some silicone into the holes before you screw it back on. You should not need run a bead silicone on the actual rubrail.

Easiest confirmation is If you pop the engine hatch when you have everyone in the boat, you will probably see water coming in at the seams...3m Silicone will stay flexible and seal up the seam where the hull and deck meet and each screw should be pulled. Using 5200 will work but if you have to replace a section of the rub rail backing - you are in for a fight to get it off (5200 will hold trim tabs to a hull so it will definitely hold a rub rail).

Long story short, your in for a bit of a job but you have to seal the hull/deck (behind the rub rail) and each screw hole

If he uses 5200 to stick the rub rail on, and he or somebody else ever tries to take it off, they are liable to rip up the shoebox joint pretty bad..... 5200 on the hull to deck in the joint is good, but make sure its cured before installing the rub rail.