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I tried looking for your hull in the DWG's on Boston Whaler site but, the cut off date was 1998, so no help there. Well maybe: go to that site and get to the DWG's and look at the 1998 model to see if that looks like what you have or not. If you can take some pictures of the drains that you have and post them, we can see the problem. Sue at Twin Cities may send you a copy of the DWG's that they may have, just a thought. The melt water should not go to the fuel tank as you describe, should go thru the aft vertical bulkhead and I think it's a piece of StarBoard that is fastened to the boxes.
Garris- the melt water drain is just that, it allows you to drain the ice water to the bilge and get pumped out as bilge water so you do not have to open the drain in the bottom of the fish box while underway to drain the ice water.