Not to further confuse this, but with the port and stbd switches each on both, will one charger, hooked to the jumper cable plug, charge both batteries?

Yes

On another link someone stated that the grounds could be different causing a problem with the computers, but if US1's schematic is correct the only way this could happen is if there is a lot of current on the ground leg between the two batteries. One battery would have to be dead or very low and the switches on both.,,,,DUH just answered why you don't want to leave on both.

I took switches a part found starboard switch to be starboard motor batt. 1 and house batt controls cabin and fridge. port switch is port batt. 2 does nothing but start port engine.

Switches had one wire coming from each batt. to the 1&2 post then had jumper wires going to other switch. One wire from conn post going to starter. Cabin power was wired to starboard switch #1 post.

What he said!!
 

this is correct

Not to go against what was said about running on "both" but I have been for 11 years, to add to that I never even turn the batteries off when I put the boat away for the week / summer or in storage / winter....I agree with the LLL and RRR running them on 1 and 2, I will try this if its better.

Leaving the switches in the BOTH positions removes your option to start your motors if you spend all day listening to your stereo and you run your battery down. Opps I mean running BOTH of your batteries down. :) In the BOTH position, you don't have 1 dead battery, you have 2.

I never turn my batteries switches off either. Only time I've ever messed with them is when I've had a battery go bad.

Makes even more sence....

Just pulled out one of the Merc Manuals, Section titled "Multiple EFI Engine Battery Precautions" (not going to type the whole thing, just the highlights)
"EFI Electronic Control Module (ECM): The ECM requires a stable voltage source. During engine operation an onboard electrical device may cause sudden drain of voltage at the engine's battery. The voltage may go below the ECM's minimum required voltage. Also, the alternator on the other engine may now start charging. This could cause a voltage spike in the engine's electrical system. In either case the ECM could shut off ..."
"Batteries: Boats with multi engine EFI power packages require each engine be connected to its own battery. This ensures that the engine's ECM has a stable voltage source."
"Battery Switches: Battery switches should always be positioned so each engine is operating off its own battery. Do not operate engines with switches in both or all position. In an emergency, another engine's battery can be used to start an engine with a dead battery"
The 500 EFI manual included a paragraph for multi engine applications that says running with switches in both or all position can cause voltage spikes or unstable voltage that can permanently damage the ECM.

Thanks, good info....1 and 2 it is then

Good info indeed. Thank you to all who took the time to post replies.