Probably you have already done your floor by this time, but just in case... First 1/4 inch out of level is no big deal. You don't need to level the floor, otherwise I would suggest a mud job. You can float it and then set your tiles on thinset. It is very important that your subfloor is solid, otherwise your tiles will crack. If your subfloor is not CDX plywood and you have one-by boards I would recomend to install 3/8 plywood over and instead of wonderboard use 1/4 tile backer boards. These are installed like wonderboard over thinset and instead of using screws you can use 1-1/2 galvanized roof nails. You are supposed to tape the seams with a vinyl mesh tape. Also allow a 3/16 gap by the seams for expansion.