5200 is VERY messy stuff, and is far more than just a sealing silicone. It is very tacky, clean-up is difficult, and it is very permanent. (I've seen it rip large areas of gelcoat off a fiberglass boat when a jackplate was removed.) The "get it everywhere goo factor" of 5200 is not easily expressible.
What you want to seal is for convenience, not critical integrity of the boat. Academy also sells a tube of 3M clear Marine silicone sealant that I have used quite a lot on my boats and I've found it to be adequately tenacious in not letting go, even on slick gelcoat. I suggest you do as much as you can to push the sealer into the seam, even using gloved fingers to force it in further. Cut the applicator tip at a small diameter so you can get the product aimed into that seam as well as you can.