If you plan to carry spare tires on the roof, I would suggest you get a roof rack basket. It will keep the tires from damaging the roof, and give you better support and points to tie them down.
As for the 2nd part of your question, not sure what you mean by the "spare tire well". As far as I know, the only factory spare storage is under the rear end of the vehicle. If that is what you mean, I don't think you can fit a 2nd spare under there. Even if you manage to hang two tires together, I think it would be too low and cause ground clearance issues.