I don't have much time to reply now, but your questions are so intriguing. I will definitely give them some thought.

If the Kryptonians needed to be contained within a geographic area, there are a couple of possibilities: some multi-national organization (like the UN) could designate an area. As Lynn mentioned, it could be an unpopulated area given up by consensus of the prior owner.

If we're talking just about the US, one thing that came to mind was turning an existing national park into a Kryptonian Reservation. Inside the boundaries, they would (in theory) be a sovereign nation, similar to native American Indians.

I don't think it would be too hard to imagine the Kryptonians getting restless. Being relocated multiple times, having their movements and/or lives restricted, getting long-term illnesses due to constant, low-dosage Kryptonite exposure (in the water supply, maybe?) might do it. I would think that the degree of dissatisfaction would have to do with how far they had fallen and/or how badly they are treated afterwards. Do they have some semblance of freedom or is it more like a work or concentration camp?

Question: why wouldn't Clark be forced to join his people once he was outed? I can't imagine any government keeping a Kryptonian invasion quiet, so the people of the world would know of - and probably be frightened of - what one free Kryptonian could do. Why is Clark trusted to roam free?

Sounds like an interesting story. I hope to read it soon.
BJ