Whew! At least that bit of confusion is laid to rest. Now, Tanyarae. I'm not sure I hav a clear picture of your problem, but maybe this will help you determine what has to be done. A flange set on top of the finished floor. It is slipped over (sometimes into) the drain pipe and is glued to the drain if the drain is PVC or ABS pipe and lead to it if the drain is cast iron. Screws are inserted through the flange and down into the subfloor. This anchors the flange solidly to the floor. The flange has two slots for tee bolts on each side that hold the toilet down, so the flange must be oriented properly so the toilet will set square. A wax ring or a new style waxless ring is placed on the horn shaped projection on the underside of the toilet and the toilet is lowered onto the flange making sure the tee bolts are through the holes in the toilet base and the sealing ring directly over the flange opening. Seat the ring by downward pressure and gently rocking the toilet until it rests firmly on the floor all around. Apply the nuts and washers to the tee bolts and tighten just enough to be firm. There should now be no rocking or movement of the toilet possible.
Now, what you have to do to get to the place where you can do all of the above is impossible to tell with the information given. Not to doubt your determination to DIY, but this may be something better given to a professional. A toilet drain is certainly one job that must done right to avoid a multitude of future problems. If there is an "easy" way to do it, a plumber will know what to do and how to do it. If there is not an easy way, a plumber will know the best way to do it properly.
