bathroom tiling

I\\\'m laying porcelian tile in my bathroom,and have several questions.
When preparing to lay the tile,should i raise the toilet flange to tile under it?
What kind of caulk or grout do I use where the bathroom meets a wooden floor? What do I use against the shower stall for grout? or do I use waterproof caulking?
Thanks

Definantly raise the toilet and tile under it. This makes it very easy to grout and caulk. Use a grout that is designed for bathrooms or "heavy water" areas, and yes, use waterproof caulking. I just re-did a bathroom and did it this way. Things went very smooth!