Warm storage....
If you've got the battery and boat in an area that is protected from freeze, then you don't have to remove the battery.
It's not your imagination on the battery drain. Lead acid batteries are always in a constant drain. If you have the battery connected to the boat, as it appears you do, then you need to disconnect the ground cable at a minimum. This will break the circuit and allow you to hold a charge a bit longer. The computer (mpem) will not be affected. It retains all its information even with the battery out of the boat.
Do not use a battery charger on the battery while it is connected to the electrical system, unless you are charging at 2 amps or less. Over charging the battery causes gassing and is explosive. A battery tender is the best way to maintain the battery. It automatically comes on and off as needed by the batteries needs. You can also leave the battery connected while in use. But, in my opinion, I disconnect my batteries when not using. Having a PWC, makes this harder, that's why a tender is an excellent idea for them.:cheers: