That is a tricky one. Depending upon the type of in floor heat you have you will need to know exactly where the heater is located in the floor. This can be done in several ways.
The hard method would be to break up the floor and hope you do not damage anything under it.
The easy way would be to turn it on and find a contractor, perhaps a home inspector who uses a infrared camera. The camera will locate exactly where the elements or pipes are located so when cutting the hole for the flange you will not cut into the pipe. We use ours for this exact same thing when were looking to find a damaged pipe in the floor.
Good luck with this. It can be done, but do so carefully.
I was hoping to go above the floor with the plumbing. The room is an art studio attached to our home, like an attached garage would be. I have a sink for washing my brushes etc. so I was hoping to connect to the existing plumbing someway.
You would need access to at least a 3" main drain line to connect. You could construct a step up box to rest the toilet upon if you like. Then just fasten the box to the wall and glue it to the floor. This would depend upon the location of the drain line.
Watertown....I used to drive through all the time on my way to St Lawrence. I put myself through school fixing houses from Canton to Watertown....have you thought about one of those incinerating toilets? I don't know much about them: http://incinolet.com/
Thelma we love our chair height toliets. It sure helps as we get older. Of course you have to think about if you have children or grandchildren because they may be to high for little ones.