Bathroom floor question

I remodeled my bathroom a couple years back. I'm happy with most of it, but I really screwed the floor up.
I tried to lay tile. I made several mistakes here. I was told it was ok to put it down right on top of the linoleum. It has always floated around.
The big problem though is around the toilet. The ring that holds the plumbing for the toilet had rotted. I thought I was being smart and bought another ring, cut it, and slipped it behind the base (to keep the base from slipping below the floor line. I have always had trouble keeping it sealed, since.
I'm ready to make the big commitment. I'm ready to rip out the floor, rip out the toilet, cut and reinstall the plumbing if I have to.
Is there a way around not cutting out and reinstalling a new base for the toilet?
When I install a new floor, should the toilet attach to the sub floor and the flooring come up to the already mounted toilet, or should I mount the toilet onto the new flooring (I'm thinking of tile or a floating wood)?
Any help is appreciated.
Scott
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You will need to repair any failed wood substrate, add a new flange and do your floor-covering. Most modern toilets mount to the flange. You say your flange was rotten so that makes me think you had a metal one. Is the pipe blow the flange lead or plastic pipe? Or how old is the plumbing? A little more detail from you and one or more people will post help.
I will add that if your wooden floor is not rotten there is a repair flange available at full service plumbing stores that works fairly well.
Colbyt
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Yes, the outer flange was metal. It looked like it was to sit at the very lip of the flange. The rest of it is plastic. It didn't really sit flush though. It is above the level of the floor. The plumbing is about 15 years old. There is some bad wood there, but there was enough (at last glance, that everything was still secure and firm.
I'm still confused on whether the toilet (and flange) will sit on top of the ceramic tile or floating wood floor, or whether it will all mount directly to the substrate and the tiling (or floating floor) will then bump up against the toilet.
Thanks Scott

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The flange sits on the sub-floor where it is securely anchored. The tile is cut around the flange, but where it will be covered by the toilet.
If the plumbing and sub-floor, is a-ok, you should be able to refloor or clean the bath simply by pulling the toilet off, and you have full access to the floor material.
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