If you are talking about the overhead hatches, I would check the screws holding the hatch. I had a leak on my boat (2000 H340) and found that some of the screws had stripped their hold and the caulking had failed. I relaced the screws with the next larger size and applied plenty of caulk into the screw holes. You can also run some caulk around the edge of the hatch where it meets the deck.
My preference for maintenance caulking is Captain Tolley's creaping crack sealer. Available at West Marine, it is a thin fluid that "creeps" into small spaces (like where caulking separates). I use it to seal and maintain my mast base and hatches and every item attached to the deck.