Plumbing Questions? Ask a Plumbing Expert.
Hi, I'm happy to assist,
The flange should generally sit flush on top of finished floor, if you lowered it more than that you may have made it worse (maybe 2-wax rings needed-see below). But if that's not the case;
make sure all of the old wax is removed from the flange and bottom of the bowl, look at the flange and bowl bottom to make sure there are no cracks in either.
Since you're having a leaking problem, I would get a wax ring with the horn in it. Sit the wax ring centered on top of the flange and carefully lower the bowl straight down over it while lining up the 2 closet bolts. you should feel when the bowl starts to touch the wax, at that point slightly twist (not rock) the bowl about an inch in both directions while pushing down at the same time, do not lift bowl and start over, if you do at any point, you will have flattened the wax ring and it won't work. Once the bowl is down as far as it will go, place the closet bolts nuts and washers on and snug them up, at little on each side at a time, rotate with each side to pull it down as evenly as possible. If the bowl rocks after the nuts are (gently) tightened, you will have to shim the bowl, but try not to lift the bowl much at all if shims are used, loosen the nuts just a little and place the shim only where needed, the re-tighten.
If by chance your flange is now too low, one wax ring wont work, sometimes we use 2 in those cases if we feel that will work, when I use 2, I use one horned wax ring and one plain wax ring, I place the flat ring directly on the flange, then I place the horned ring on top of that one, with the horn going into/towards the inside of the pipe, then use the same procedures described above.
One final note: sometimes a leak coming from the underside of the tank will appear like a wax ring leak. it could be hard to see, I usually make sure my hands are dry and feel for these types of leaks, a flashlight would help as well, even with the bathroom light. Just in case, check the bottom of the tank where the 2 tanks bolts come thru and in that general area, you may find that a slight drip/run working it's way down to the floor, appearing as a wax ring leak, if so, try tightening the tanks bolts. While down there, double check the supply valve and line for leaks.
Hope this helps,