Dickauge:
What is your protocol for charging your batteries under way; and, at the dock. What's your general practice of use, etc.
It's not at all unusual to have two batteries and a 1-BOTH-2-OFF selector switch. What is a bit unusual is to have two different batteries for the two banks without some other provisions. IT CAN WORK -- but it would be best to understand how you use the boat, etc.
If the "Engine Start" battery (as you describe it) is just back-up, that's different than that's the one that you plan on switch to when you start the engine. Then, how you use the boat (your loads from equipment, cruising patterns, shore charging, etc. becomes more critical. If you had two of the same batteries (WHICH YOU DON'T), then the OLD practice that we used decades ago went something like:
On "even numbered days", use battery bank 1; and on "odd numbered days" use battery bank 2. That was based on having the batteries charged by a regulator that could charge two banks independently or a combiner (of sorts).
You left your batteries on 1 or 2 -- and you avoided BOTH. If you didn't have dual charging capability, you could charge on "BOTH", but only leave the switch on one- or the other.
There are work arounds -- but it depends on YOU, how much attention YOU pay to what your doing, and HOW YOU USE THE boat and its systems.