Ah, then you know your way around boats, CLV.
Your dealer's comment: "if the one battery is low then the alternator doesnt see a low charge because of the good battery voltage". I don't think that is correct. When 12v batteries are wired in parallel they become one big battery but still supply only 12V to the load(s), and it doesn't matter how many there are. However, when one battery is fully charged and the other is discharged then turning the switch to both will cause both batteries to be less than 12V. In otherwords, if one is at 10V and the other at 12V you end up with one big battery at 11V. From what I've read it doesn't happen instantaneously, but how long it takes depends on how discharged the one battery is. Voltage from the charged battery flows into the discharged battery. Regardless, The engine's alternator still only "sees" one battery and is going to charge it.
I make my "which to run on" decision based on a few things, like how long has it been since I used the boat and, therefore, the relative state of charge for each of my two batteries.
I have 1 regular lead acid battery (Batt 1) which is generally my start battery, and one AGM (Batt 2). AGM's don't discharge from non use as quickly as LA's do. I start up on B1/lead acid and run to whereever I happen to be going to get it charged back up. Drop anchor/tie up and switch to B2 (AGM). Back to B1 to re-start, then switch to Both for the run back to the marina. Or, if my run to where ever will take an hour or more I run for about 30 minutes on B1 then switch to both.
The first season with the boat I had only the lead acid battery - which was installed new when we bought the boat. I installed the switch and the AGM in the spring of season 2 and have been operating the boat as discribed above for 3 seasons, which makes the LA battery 4 years old and the AGM 3 years old.