I discovered a leak in the base of the upstairs toilet that had soaked the subfloor and cause the tile to come loose. I removed the tile and discovered that it had been set on a plywood backer. I removed the plywood and cut out the rotting wood around the toilet. This exposed the ABS plumbing below, which appears to be in good shape. I bought a new aluminum flange that supposedly allows me to cut the drain pipe flush with the floor. I have read in other threads that the flange should be placed on the finished floor. I intend to install a concrete backer and retile the floor. How do I screw the flange into the subfloor if it is sitting on top of the new tile approx. 3/4" from the wood subfloor? Do I glue in new ABS pipe and leave the flange unglued until the floor is finished? Also, how do I level the flange taking into account the slope of the underlying drainpipe? When I glue the new elbow onto the existing ABS it will present an angle that will ultimately put the flange at an angle. Is there a standard way to deal with this?

I discovered a leak in the base of the upstairs toilet that had soaked the subfloor and cause the tile to come loose. I removed the tile and discovered that it had been set on a plywood backer. I removed the plywood and cut out the rotting wood around the toilet. This exposed the ABS plumbing below, which appears to be in good shape. I bought a new aluminum flange that supposedly allows me to cut the drain pipe flush with the floor. I have read in other threads that the flange should be placed on the finished floor. I intend to install a concrete backer and retile the floor. How do I screw the flange into the subfloor if it is sitting on top of the new tile approx. 3/4" from the wood subfloor? Do I glue in new ABS pipe and leave the flange unglued until the floor is finished? Also, how do I level the flange taking into account the slope of the underlying drainpipe? When I glue the new elbow onto the existing ABS it will present an angle that will ultimately put the flange at an angle. Is there a standard way to deal with this?

You have me a little confused. How do you "glue" a aluminum flange to ABS pipe?
You ask, "Also, how do I level the flange taking into account the slope of the underlying drainpipe? When I glue the new elbow onto the existing ABS it will present an angle that will ultimately put the flange at an angle. Is there a standard way to deal with this?"
The standard slope for drainage is 1/8 to 1/4" per foot. You can't cock a toilet stup-up and expect the installation to be leak free. You're going to have to level the horizontal pipe to a acceptable slope and then raise up from the elbo. You may then glue on a regular ABS flange after you cut the stub-up off level with the floor line. Good luck, Tom