If you mount a capsule - does it automatically put a Kerbal in it each time? Is it possible to have unmanned capsules?

Yes. I have a conscious..

Put an additional flatsat between the capsule and the chute for control, unload the Kerbal before launch, then switch back?

...Pretty sure there are mods for that too!

I think I read that it used to but that now with the crew management in .21 you can chose if anyone goes in. Haven't had chance to try .21 yet though. Busy busy busy. In .20 I had one of three Eva on the launch platform so thered be room to rescue my stranded kerbal. It worked!

You can have an unmanned capsule but your ship will be uncontrollable. I tried and that was the message I got. I'm using ver .21. I finally made my first landing on Minmus. But unfortunately on the way back I ran out of fuel so my Kerbal is stuck in a Kermin orbit. I'm going to attempt a rescue using a larger capsule and removing one of the Kerbals. Of Course I have no idea how to accomplish this. I have the ship but don't know if I'll be able to get close enough to the orbiting capsule since I can't dock with it.

If you want to save kerbal lives use the probe cores.

There are also crew transport modules by stock parts which you can put on your rocket and use as extra storage to recover kerbanaunts.

Thanks, I'll check those out.