Lots of options
I recommend you look at books by Nigel Calder and Casey on boat electronics. The simplest way to arrange your batteries is to have a house bank and a separate starter battery. They could be wired with a traditional 1, 2, both, off type switch (Is that what you have now?). Start the engine on starter battery, then switch to both and charge both battery banks simultaneously on just charge one bank then switch to the other through both. Having an amp meter would be a simple way of knowing when the batteries are not taking a big amp charge and you can switch to the other bank. There are advantages and disadvantages to this. Cheapest, but least sophisticated. Don't mix different types of batteries. I assume you have one alternator on your engine and the output wire is wired to the both terminal on the switch. The solar panels also could be wired to the both terminal but might just be wired to the house battery. Make sure you read about the importance of proper fuses to prevent fires.
A more sophisticated system would be to put a charge combiner between the two banks and the alternator output to one of the banks. A charge combiner serves to isolate the banks from each other when a load is sensed, and parallels them when charging. This replaces the standard 1, 2, both and off switch. Each battery would have its own switch. The combiner has an emergency parallel in case the automatic function fails.
A great alternative is to have 2 alternators, one for each bank. I'd only do this if you are planning some serious cruising and have significant energy demands.
I have had boats with all three of the above described systems. Option 1 requires the operator to think about when to switch from bank to bank, but is no big deal. Option 2 and 3 work independent of operator input.
Other issues to consider are choice of battery type, charge controllers, shore chargers, and your solar charger configuration.
Mainsail is a real expert, and hopefully will join this thread.
