this might be redundant, as I dont know jack about the specific boat...
1. You want water to move thru the channels to a drain... perhaps all you need to do is drill a couple of small holes in the channels and then route (use aquarium tubing) the water from there into the bilge area.
2. Seal the lids better - add an "o ring" to the top ridge to help keep the water out.
Both of these ideas assume there is a channel with something "raised" on it... hell, if there isnt already something raised, perhaps adding the "o -ring" would be all that is required... something of a barrier.