How did you seal that tray? It seems to me it's flimsy and suspect for taking on water for sure.
What
@Babin Farms said, caulk, will work fine. I can't remember who it is, but someone on here used some closed-cell adhesive-backed weatherstripping and some speed nuts to get an easy-to-remove seal on his hatch. I got the weatherstripping, and I'm going with longer screws instead of the speed nuts. If you decide to go with the caulk just for proof of concept, you can always remove it if you find or figure out a more permanent solution. It should peel up pretty easy, and you'll have to use some acetone to remove the residue left behind, but it's easily reversible/changeable.
I've never owned a boat before this (and now I have my dad's fishing boat and a skiff), so as long as you are here, ask all the questions you need to map out your project, lay out your final results you come up with to see if anyone can find any issues with your methods, and once you're satisfied/comfortable, dive on in! No matter if someone here has worked on boats before or not, everyone, at one point in time, had never worked on a boat before, and was in the same position you are. You think you're at a disadvantage, but the only thing you lack, is your first successful project under your belt. Seal the hatch with some caulk first, and you've got an easy win. WAIT! DON'T seal your hatch first! That second bilge is gonna be easier to install if you can remove that whole hatch panel, it'll give you way more room to reach in and get around. Sealing your hatch is a good finish to that project. Best first project, unscrew one of the snaps from the carpet. If you wanna keep the carpet, screw it back in. That's two things to check off on the To-Do list
If you've got a smart phone, TAKE PICTURES OF STUFF AS YOU ARE DISASSEMBLING THEM! Just DO IT! The time to realize you should have done this is NOT after you're up to your elbows in this. Before owning my boat, I had never had more than two cables coming off of a battery before. Glad I took pics when removing the battery for winterization. Woops, that's right, no I didn't
You have an awesome resource at your fingertips - this forum. I was able to figure out how everything went back together by checking around here.
You can do it!