I doubt Grady wired the boat in manner that doesnt allow for the house batteries to get recharged by the engines. The Marlin has 3 independent electronic systems (in a sense) One for each engine and one for the house electronics. I've drained my house batterries down several times and recharged them while running. I cant comment on how yours is set up, but mine is a factory set up and it works great. I have 3 batterry switches; one fore each engine and one for the house batts. Per the dealer where I bought my boat, I run each engine battery off of its own batterry (port engine to batt. 1 and sb engine to batt 2. The house batts have a simple on/off switch. I ALWAYS turn them off when not in use. The charger should do its job if its working the way its supposed to.
Another thing to consider; if the batteries are dry or dead, they might not be taking a charge from your engines or not holding a charge etc. I ran into this prob. with dry house batteries. The shore power charger will work overtime to charge a dry batt. and can poss. kill or weaken your other batteries, while never even charging the battery that needs it most because it can't if it doesnt have water.
try charging your batts with the engines only, not the shore power and see what happens. Or have your batts checked. Not a small or cheap task
hope this helps
good luck