With the can type solenoid I have, I think it just isolates the start battery when the ignition is off. Im pretty sure that when the engine is running and the ignition is on that they are connected in parallel and both charged.
I would agree with you Jas. They'd behave just like one big battery.
I'm with the others, I've got my winch wired to the main battery. I've got the ability to connect the main to the Aux around the isolater - it wouldn't be my preference to do this for winching, but it's certainly possible. I've started the car off the Aux before - again, not good for a DC battery, but it managed it fine and hasn't seemed to have affected it.
As GG has said, I think that so long as the car is running, if you stick to the winch's duty cycle, then your alternator is going to be able to make up the shortfall in power supply pretty quickly. The trouble comes in when you need to winch for a long continuous time for some reason, or if the motor has stopped and you've only got the one shot at getting out. But in either situation, you're going to be in a "do whatever you need to and bugger the consequences" type of mood, if it's serious enough that you can't just secure the car and go get help.
Reminds me, I need to rewire my winch...
Good luck!
Matto