A solid wood floor in a bathroom will look beautiful when finished, but keep in mind that wood may not be the best material in the long run for a bathroom floor.
Bathrooms are by nature wet, moist places, and that's why materials like tile or cut stone are popular. Unless properly treated and sealed by professionals or prefinished specifically for a bathroom floor, a wooden floor can develop moisture problems, especially under the toilet. Make sure the floor you choose will work for a bathroom. If not, go with another choice.
If you are using the existing toilet flange that's level with the present floor, it will have to be raised up to be level with the new thicker floor. Get flange extension kits from a good plumbing-supply house. They will attach to the present toilet drain and raise the flange height. Once you raise the flange, cut and seal all the flooring around the new flange to complete the job.
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If you are completely running a new toilet drain and you have open access underneath the bathroom, call a plumber to help you. Running a new toilet drain is a job for the pros. Install the wooden floor first and mark the location for the toilet drain, making sure to avoid any floor joists. Then the plumber will drill a large hole right through the new wooden floor and the subfloor, making a neat clean hole.
A bathroom usually consists of two main parts: a bowl and a tank. It is best to first install the bowl. Prior to seating the bowl, check if the closet flange has been temporarily plugged with insulation or a rag to prevent sewer gases from escaping. Remove this. Next set the bowl on top of the closet flange to determine if it sits level. If it does not, prepare some shims to use later.
A special low-profile flat flange is now screwed tightly to the new hole, and the toilet drain piping can be run underneath the floor to the new flange. This is a truly professional job. It now appears that the flange is built right into the new floor and it's locked in place. Toilet flanges should sit level or right on top of a finished floor for a good seal. Having the flange too deep in the floor can put you in deep trouble.