I have a blue seas battery isolator/switch that is linked to an ACR.
What position should the battery switch be in/on(OFF,1 starter batt,2 combined batts)for charging both batts at once/together?
ACR always makes sure stater batt is at full charge then surplus  charge is feed to the house batt then switches back and forth between the two batts whilst motor is running.
Have just hooked up a easy connect plug in that fits both sets of batt posts.
Once I have this nutted out,I hope to just leave batt charger in/on for a maintenance/float condition.
Cheerz  

I have this same system and run 3 batteries. I only have it on "1" and the ACR charges all three. When I bought the boat I queried the same from owner and seems to be fine this way. I'm no expert but starter battery always get first charge and then other batteries follow afterwards.

Little different.. smaller scale.
We have 1 main battery...like any ave day boat.
But always carry a spare jump battery unit.
When staying out over night I turn off the battery isolating switch to the main battery.
Plug the cig lighter accessory off the portable jumper unit into the cig lighter on the dash.
This then runs the lights, gps/ sounder, radio, and rear deck lights for fishing, overnight.
The cabin internal lights are dual fluorescence, the rest are led.

Next morning,  I turn on the main battery, then disconnect the cig accessory plug, fire up the engine , then plug the cig connection back in.....the engine now recharges both batteries.

Do not start the engine with just the cig plugged in and main not turned on... the starter is a huge current draw and blows the cig circuit fuse.
I have not tried with main battery and jumper connected thru cig to see what happens....Dont need any future hassle of a weakened fuse blowing , as per murphys law at the worst time.

The switching of a duel battery setup I would imagine to be similar...

If u have a duel setup and 1 battery is getting low from over night... and would most properly have to be too low to run a gps/ sounder (???)  if turning both on to fire up, dont mess around before firing up.... when flat and charged battery are hooked together they will balance out their charge.. but one the engine alternator is running it will recharge both...

And a side note on charging batteries.. many types of chargers will not chargea battey below as set voltage, arounf 9/10v.. they are programed to assume the battery is a dud.
To get around this , start charging a good battery, and while that charging, them put jumper leads to the dud battery... the charging voltage stays high, wait for a couple minutes and disconnect the good battery if charged....will carry on charging the low battery nps.

Reel Deal.
With my batt isolator/switch it goes something like this with the twin batt setup.
OFF= islolated both batts.
1   = power from starter or #1 batt.
2   = combine power from both batts to feed #1 batt to turn over motor(emergency backup)
ACR senses current from alternator,tops up Batt 1 first the feeds excess current to Batt 2.
At rest using electronics, ACR draws down power on Batt 2(house batt) first.
ACR starts flashing when voltage gets low on Batt 2 at rest so skipper knows to power up boat.
This should still have a full charge in Batt 1.
Still need to be able to see the small led flashing to warn you though.
Make sense?
Cheerz

what is an ACR?

BEP do a VSR (VOLTAGE SENSITIVE RELAY),  the idea is that when the start battery has reached charge the current from the alternator is then sent to top up the second battery, it is a good system provided you have a big enough alternator. Some outboards like mine only have a 7 amp alternator and it is a struggle. Just hook the smart charger to the start battery.

A VSR works like this, you have 2 batteries, With your 3 way switch you select 1 battery to run from while sitting at anchor so the other battery stays charged if you need it to start. When the engine starts and the voltage gets to a level the VSR joins both batteries together so both are charged. When the engine is turned off the voltage drops down under the level the VSR drops and disconnects the 2 batteries from each other. You are left drawing from the battery you have switched on.

In larger boats you can run a deep cycle house battery for running off at anchor and a high discharge starting battery for starting. In my boat I run 2 normal marine starting batteries, I run out fishing on one battery and leave that one switched on to run lights and electronics while I'm anchored then I switch over to the other battery when I head home. If needed I can join both batteries together with my battery switch if I need the extra crank. Have never needed to because I use a ctek charger at home.

This is a pretty standard setup.

As long as the voltage meets the right voltage level the VSR will kick in and charge both batteries. I don't do this on my tinny, don't like the battery being left on. I turn the battery switch to off and just change the battery charger over to the other battery every couple of weeks. Use the Ctek battery indicators the ones with the three LEDs on both batteries. They are really good and let you know where the charge of your battery is at a glance. Also a quick way to plug the charger.

Interesting comment about the different algorithm, never had that problem with the batteries you use.

There are proper dual battery solar regulators. That is what you need. Connecting a single output regulator to both batteries is like wiring the two batteries together.

Im not a big fan of sola panels, you need to have a very high quality unit to have something that will be trouble free for a long period. Good ones don't come cheap and add the cost of the regulator and your up for some real money. You cant beat the Ctek units to keep your battey in good condition.