K,
Why do you keep the battery selector set to both, when not at the boat & having to run systems, this should be off. I can see if maybe your bilge pump is wired this way however, there may be some other unknown circuit problem which is draining power.
You want your bilge pumps wired directly to your batteries to avoid problems.
Secondly, I installed a digital battery charger. I have AC receptacles hooked up & wired to my shore power thru a breaker. I do have an auto-manual switch on my panel but the juice goes directly from shorepower to battery to pump.
I take the plug from the charger & plug it into a good China Depot house timer, simple.
I have my timer set daily for 1 1/2 hours. When the timer goes on, I get 5 minutes of full charge & the rest becomes a trickle charge. This keeps my batteries up without cooking them. If using wet cell with caps, that's a poor choice. Remember only use sealed batteries.
In addition, there is no reason other than price to have wet cell-non sealed batteries on your boat. I myself use only ATM batteries. I find they charge easily & I get between 5-6 years use. Sure you pay more upfront but, it's worth it pal.