I replaced my bathroom linoleum floor with tile. I was using a flange extension to raise the toilet. I have 2 questions:

1) Do I use silicone between the extension and the flange to seal it?

2) How high do I make the extension? Should it be exactly the same height as the new floor? Or should it be a little higher? Or a little lower?

Use a PVC spacer to raise the flange so the flange top surface is flush with the surface of the floor. You can glue the spacer with PVC cement, silicone it or use nothing like most people.