So I recently purchased a Grumman aluminum boat, and gave it a overhaul. I rebuilt all new decks, gave it a fresh coat of paint and got it all ready for this upcoming season. I added storage compartment in the front and back decks for all my tackle. The only issue that i have noticed is that when in the rain, water leaks into the comparments. I was wondering if anybody had any tips or suggestions that have worked for them. Thanks for all your help. 

Sorry I can't help you with your issue, but seeing
you are new to the forums, welcome aboard!

Water will work its way down in the joint between the lid and the deck. If there is not some sort of lip or flange that redirects the water some of it will end up in the compartment. On my stratos it's basically a raised fiberglass ring around each compartment that creates a channel that directs water to weep holes that allow the water to go to the bilge.  The lid closes around that flange. You could create that flange perhaps with some automotive weather stripping.  I suck at explaining stuff but hopefully that makes sense. 

look at using 2 part marine foam to direct the water to where you want it to go 

You need a "gutter" at the bottom of the opening and around it.  Then, you need a drain tubing at the lowest point that leads to the bilge.  Most fiberglass boats have it molded into the deck below the hatch.  Something like this.

Go get some adhesive weather stripping from your local hardware store, I'll send a picture of what kind to get in a later posts I do this on all of my boats, just to help. But it is a good way to seal off a comprtment, put it around the edge of the opening so the lid creates a seal when it's closed jut like it works on Windows and doors in your house.