I have run both single and twin engine 2 battery boats for 20 years. All boats had two batteries with one or two Perko switches with "1, ALL, 2, OFF " positions. I own three 2 battery boats right now that all get regular use. My experience is from a total of 8 different boats. Formulas, Fountains, Sea Ray, Marlago, Baja.

I have always used the same system: Battery switch(s) on 1 the first half of the outing, and on 2 the second half or on the way home. I make sure both batteries start BOTH of the engines, one at a time, on every outing or I charge or replace the low battery at first opportunity. I never use the BOTH or ALL position unless I have a problem starting which has been very rare over the years. For sure, absolutely, I have never had a problem using this system.

The only battery problems I get is when I pick up the boats after service it seems the repair people always leave the battery switches on ALL and I have had two dead batteries several times because of this nonsense. Now I check the switches before I even leave their parking lot and will make a comment about why I am getting into the boat!

As far as your charging voltages I would get a good quality meter with long 16-18 gauge leads clipped to each battery one at a time and watch the meter during operation to see if it agrees with your dash gauges. Check your ground and electrical connections - a bad ground can cause an otherwise inexplicable problem. And of course alternators and voltage regulators do fail, that's why the check while under way with a good meter.