Knot holes in plywood for second layer of subfloor

This is my first of 4 tiling projects (all floors and all going over vinyl flooring). I started with kids bath (not even 5'x6'). I removed all molding and thought I'd tear up some vinyl. Discovered that its very thin and can come up pretty easiy, but would prefer to avoid the work. Thinking about screwing through vinyl to further secure subfloor, then install 1/4" hardi backer board down and then 3/8" tile. Questions are 1) how to I transition to carpet (1/4+3/8=5/8 height) which comes all the way to the edge of the jamb on inside of bath. Do I buy a marble threshold and cut it in between the jambs? (I dont want to cut the jambs, don't have the tools. 2) How do I handle the toilet flange? Are there "extenders" that will install over the current flange and rise the bolt locations? Will one of those super thick wax rings work? please help I want to do this next weekend. thanks in advance.

Hey: In the process of replacing some tiles in the bathroom, we applied the grout as directed and let it cure over night. There was some clean up that we missed and tried cleaning the tiles with one of those green kitchen sponges with a scrubbing pad on the back of the sponge. Anyway, some of the green color came off into the white grout..:wall: :mad: :wall: What should I do to get this out? Should I wait a few days and then hit it with a mixture of bleach and water? Help please as this is a real eye sore on this tile job that other than this Green grout line, looks great! Thanks in advance for any and all help or suggestions. Take care Dan