Live wells under the deck has always been a PITA as well as Fish Boxes.
Either one (being below the deck) will fill to the waterline UNLESS you config it with a pump/macerator to get out the. Seacocks and switch valves etc are required. (see below drawing) also overflow and a watertight hatch needs to be in the workings.
I would dump the below livewell thought and put in a watertight hatch (Armstrong) and turn it into a storage locker of some sort. A portable type livewell might be your top consideration. There are many above / portable wells available for your consideration.
Here is a link to Armstong ---------------->
http://www.armstrongnautical.com/dckplates.htm