Cary,
The guys posted some good info here for you to consider.
Having repainted my worn-out fiberglass gel coat & coloring,
the correct method is first to remove all the deck fittings then paint. This is what you have done.
I ordered Top Secret 2 part epoxy paint and after 3 years, it's still bullet-proof.
There are other(?) good sealer/caulks to use. I went with Dow Corning 795 white caulk.
It's a construction caulk that holds it's elasticity even in UV rays & does not harden. I do believe it comes in colors also.
5200 will harden & crack in time & it's a ***** to remove. Only use 5200 ie: below the waterline or, when you never EVER have to take it apart again. Silicone is a NO-NO on topsides. Silicone being a petroleum product, will shrink & pull away from surfaces, it's great at staying together with itself & harder to remove the residue.
There are equal products on the market like butyl tape etc, but I believe it only comes in black & I have never used it.
CR