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Sounds similar to my 1989 22" Outrage cuddy. I plug the bottom drain as it allows the cavity to fill when at rest. I do not plug the rear hole as I have a ping pong style one way drain that prevents splash well water from entering.

I also installed a bilge pump but rarely use it. With my set up you could leave it in the water and rain would drain to the splash well. Mine is lift kept so I could leave bottom plug out also.

Hope this helps.