I used to have a former NYC EMS ambulance (Chevy C30) as a work truck, and I completely re-wired everything from batteries to emergency lighting and here is what I did with the batteries...
The ambulance came with worn out dual batteries along with dual 300amp constant duty solenoids, and a dual output battery isolator...
I purchased a 900 cold cranking amp battery for starting the truck, and an Optima yellow top deep cycle for the vast lighting and existing external PA system (awesome for venting road rage by the way...) I chose to add a third battery, (this time a LARGE one that they put in semi rigs) and place that within one of the bays of the ambulance body - This one was to power the extensive A/V system that I had planned for back there... I then swapped the dual output isolator for a three output model to accommodate the extra battery.
The starter battery was wired directly to the starter and nothing else, save for the isolator for charging it (I figured I could manually use jumper cables to one of the other batteries in the rare occurrence that my starting battery was dead - that never happened).
The lighting deep cycle battery was wired to one of the solenoids so that I had a remote switch in the center control console to kill all lighting power when I parked somewhere (there was a TON of lights on this thing and wanted to make sure that everything was off with one switch). I even ran a bunch of relays to a trigger switch so that with a single flip I could change the lights from my custom use controls (extra flood lights, extra tail lights, grill guard mounted flood and spot lights) back to the original emergency flashing controls within the center console.
The semi battery was wired through the second solenoid so I could kill the A/V system juice when I wanted to make sure that it was off as well.
About the time I got all these modifications done, gas jumped over $2 a gallon, so I stopped driving it, and got rid of it a few years later...it got 8 miles to the gallon...yes, 8 (at $2 a gallon it cost me $40 to drive it 100 miles)...and that was double what it got before I upgraded to a header/dual exhaust system with AeroTurbine mufflers with 3" pipes...LOUD!!!
I do not think this was useful to you at all, but felt the need to share the story of my shrine to automotive wiring overkill...did I mention all this battery wiring was done with 2/0 welding wire...?
I would say that you should definitely plan on using a battery isolator if you are planning on dual batteries. If you think you will be draining one more than the other for some reason (big sound system or power inverter while the engine is turned off), choose one battery for that purpose, and leave the other dedicated for starting the truck, and every other OEM power need. As long as you buy quality batteries designed for each purpose you should never have a need to tie both batteries together.
If you require additional "run time" for the system that draws a bunch of power while the engine is off, then plan on buying an additional battery(s), and wire them in parallel to the battery designated for this purpose. Your isolator will still work the same - independently charging both the starting battery, and the "accessory" battery bank...
I feel that the only time a solenoid would be a good idea is if you required a remotely controlled "kill" switch for either of these applications. I liked the peace of mind of "killing" juice to all of those 2/0, high-amp, long length cables when I was not around. Plus, I was worried that the gear reduction starter for the 454 big block would pull than 300amps (what the solenoid was rated for) when I tried to start the ambulance in the winter - so I did not run this short power run through a solenoid.
I guess you could use a solenoid to remotely tie two batteries in parallel, but it seems like a significant expense over what a good high amp starting battery would cost - just keep all of your high-power draw accessories wired to the other battery.
Also, keep in mind that if you tie both isolated batteries together, you are defeating the purpose of the isolator, and I am unsure how the isolator (or the alternator for that matter) would react to this output connection once the engine starts.