Designing Kitchens and Bathrooms - Repair/Replacing Toilet

I have a leak in my toilet that I just found. From the looks of the flooring it has been there a while. We have been planning on replacing the linoleum with tile as well. My question is this:
1) What do I do if I find the subfloor damaged when I pull up the linoleum or toilet (if I find that it is cracked as opposed to a leaking gasket). Can I replace a patch of the subfloor???
2) Should I lay the tile with the toilet removed and set the toilet on the tile or should I set the toilet and lay the tile to it?

Thanks in advance!

If the floor and subfloor are rotted around the flange of the toilet, you will need to cut it out and rebuild it (I would use pressure-treated wood and plywood).
Use an old blade in your circular saw (you WILL hit nails), safety glasses, and a pry bar and hammer to remove the cut flooring pieces. Cut back to the center of the nearest floor joists.
Install crosspiece framing between the floor joists, half under the cut flooring, so that you can nail the new flooring to the other half of the top of the boards.
Lay the tile with the toilet removed, because you will have to re-set the flange flush on top of the new tile floor level to get the wax ring seal at the right level under the toilet.
Use a masonry bit to drill anchor holes for the flange through the new tile.
Level the toilet with a level across the bowl when you re-set it on the new wax ring and flange. You can get plastic shims made for the purpose, or you can use beveled cedar shingles strips. Either will work.
Good Luck!
Mike