Wash the boat with the bow higher than the stern (i wash on my sloped driveway). Most water should bypass the fish boxes and drain out the transom well. The center storage box has a drain (make sure it's not plugged). Water should flow from center storage to fuel tank compartment to bilge compartment. Make sure the drain from fuel compartment to bilge is also also clear.
Water will inevitably always collect in the fish boxes. Hopefully your pump works and you have 8' long arms to reach the Y-valve in the bilge area (below the transom well pie plate). Otherwise, build a contraption that you can turn the Y-valve with (from PVC pipe).
However, chances are that:
a) Your fishbox pump doesn't work (and it's probably the wrong type of pump (i.e. not a macerator))
b) Your fishbox Y-valve is broken
or c) You replaced pump (ouch) and the Y-valve (double ouch) but one of the freakin fishbox drain hoses is clogged (I give up).
In any of these cases, buy a good hand pump and save your back, your time, and your money.
Good luck, it's frustrating.