A picture or two might help.
If I am understanding you correctly you are saying that the main chamber of the dorade box is not simply a rectangle and the aft side continues on for a ways and is below the main level.
It sounds as if you will want to plug up this 'extension' to keep water from getting in there in the first place.
"The cure for anything is salt water~ sweat, tears, or the sea." ~Isak Denesen
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