The part the flange screws on to may be a piece of all thread that can be changed for a longer one. If the stem of the faucet is not long enough now, you may have to get flatter flanges. If it is the stem not coming through the flange, I believe you can get extensions for the stem and a longer bolt to hold the handle on.
Closet flanges should always have the bottom of the flange resting on top of the finished floor. So to answer this specific question, the tile should be under the flange and the flange should be secured to the subfloor.
The toilet should sit on top of the new tile.
this
With a deep floor flange Or a wax seal with a horn and extra long Brass floor flange bolts
yes....2 or 3 seals stacked
Depends on how much you need. Sometimes you can just use two wax rings. If that doesn't do it, you can use a PVC toilet flange and use it to make up the difference. Cut it off the right height and use a wax ring between it and the old flange. You cut the old flange out and extend the pipe and a new flange. If you put backer board down first and then the tile, you probably raised the floor level about 3/4 of an inch. Two wax rings with the black funnel insert in them should be enough to seal the toilet to the drain.
Extend the Wax Ring instead. The Fluidmaster No.35B Wax Extender Kit is specifically designed for problem areas where the floor flange is 1/4" to 1" below the surface as in tile work. The cost is under $6. Some plumbing supply stores sell an extension that bolts to your existing flange. If you need an extension due to new tile work, this will do the trick. If the flange is only one quarter inch or less below floor level, you can just use two wax rings.
yes the tile has to be fixtures and then put the tile
tile should slope sightly down toward the drain and drain should be recessed slightly below the top of the tile
what is the waste allowance with floor tile
yes as long if its not the vacuum ones, because it might stain your tile. best way to clean a tile is the old fashioned way with soap, warm water and a mop.
With porcelain tile you want to use a mild cleaner. Your local tile store should be able to help you choose an excellent tile cleaner. Stone Tech and Miracle Sealants make some decent tile cleaners.