ideally, the underside of the flange ring should rest on top of the floor, and the ring screws down into the floor. But it is fine to have the flange be slightly below the finished floor surface so long as you get a thick wax ring so that there will be a solid connection of wax between the underside of the toilet and the flange to prevent leaks. When you do buy a wax ring, make sure you spend the extra couple of bucks and get the thicker kind with the plastic horn/funnel that helps direct water down into the flange opening. Don't just get the cheap small wax only ring.