The lip of the flange is designed to sit on top of the finished floor and be attached through the finished floor into the subflooring. A twist-and-set toilet flange has an expandable gasket that creates the seal to the drain pipe. Depending on the one you have, it may have screw slots to tighten it or may require an allen wrench. There are usually either T-shaped slots that come in from the edges, or keyhole shaped slots that allow you to put the bowl anchor bolts through the large part, then slide it so it is captured by the large head of the bolt in the smaller slot of the keyhole.
A picture of what you have would make it easier to be more specific. Whichever way the toilet anchor bolts go, they should be parallel to the rear wall (so the bolts can fit either side of the toilet base).