Kirk
I am no expert, but I will try to help you out. First, at least I have one, if you take the battery cover to the right of the driver's seat out of the floor, there should be a black valve in the upper right corner if you are facing the front of the boat. If the handle is running straight up toward the sky, it is open. If it is parallel with the floor of the boat, it is closed. Hope your's has one so this takes car of it. Do you have a ballast pump to the tank? If so, it should keep water from getting passed it to the bags. If you do not, it could be that you have a direct line from the bottom of the boat to the bags and that is why it is filling up.
In terms of the water getting in the boat, the only thing I could think of is that your packing around your drive shaft is loose or getting bad. Again, I am no expert but hopefully this information can help.