OK I think I get it. The best thing to do regarding the 12v you want is to divide the use amperage between the two batteries, ie. instead of using only one for all 12v, use both, each for half by amperage. They should then discharge more evenly. The permanently mounted charger has three sets of leads each providing 12v or what?
As an aside, if I were you I would use 24v bilge pumps (attwood makes a 24v 1250gph for ~$60) and just get a converter for the vhf only, and run nothing else on 12v. You wouldn't need a very high amperage converter for just the vhf. Also, DO NOT use a converter like the one at the link in one of the previous replys. Make sure whatever you end up using is rated for marine use, like
this one.