Toilet flanges are usually raised up with plywood. The concrete slab will also need control joints. Control joints divide the slab into several smaller slabs, which can better absorb building movement without cracking. If the tubing doesn't pass beneath the joints, you can saw them after the slab hardens. Or you can fasten thin plastic angle strips or lightly oiled wooden strips to the subfloor before the pour.
Doorways are good locations for control joints.
With proper planning a radiant floor can fit into just about any house plan. The information in this article was adapted from Modern Hydronic Heating , by John Siegenthaler. Delmar Publishers, Albany NY, copyright 1995. A good source of information on radiant floor heating is the Radiant Panel Association. They will provide a package of information, along with a list of system manufacturers.