[pushkins]

The closet flange should be mounted on top of the finished floor, Make sure when you install your ceramic tiles that you leave room around the waste pipe for the closet flange bolts and toilet bolts. The ceramic tile just needs to go under the flange enough to support the flange but NOT restrict the floor bolts or toilet bolts.
The flange should be glued in and then screwed down to the concrete with Tapcon screws.

Many times in renovations of older work it is to difficult to remove existing flanges to lay tile, the simple solution to this is the flange spacer, available at most big box stores in 1/2" and other sizes at plumbing supply places, the spacer is simply added on top of the existing flange and the toilet bolts pass through both.