Whether you're laying ceramic, vinyl, wood or something else on your bathroom floor, you'll deal with the toilet in the same way. The toilet has to be removed, and the flooring cut to go around the floor drain. Then the toilet is reset, so the base covers the cuts around the drain. Since you're raising the level of the floor, you'll likely need to raise the level of the flange that skirts the drain as well. See your hardware store for a flange extension kit.
Things You'll Need
Adjustable wrench or pliers
Wet saw or jigsaw
Transparent tracing paper
Flange extender kit
Turn off the water supply to the toilet at the wall. Flush it several times to empty if of all water. Disconnect the water line, using your wrench or pliers. Take out the floor bolts at the base of the toilet, using a wrench. Remove the toilet, leaving just the open floor drain.
Lay the bathroom floor according to the type of flooring you're using. For hard or vinyl tiles, tile from the middle outward; for wood flooring, lay it from one side of the room to the other. Either way, stop when you get to the area around the toilet drain.
Set a piece of tracing paper on the toilet drain. Trace around the outer edge of it with your pencil, making a circle. Cut out the circle with a razor knife.
Lay the paper circle on a piece of cardboard, and trace around it. Cut the circle out of the cardboard with your razor knife.
Lay your flooring loosely over the floor drain, in the position it will be in relation to the previously laid portion of flooring. Lay the cardboard circle on top of the flooring, in the position of the drain. Mark around the circle and onto the flooring.
Cut the pieces of flooring along the marks, using a wet saw or jigsaw--whichever is appropriate for your type of flooring. Install the cut flooring so it skirts around the edges of the drain. Finish installing all the flooring.
Set one or two flange extenders from the extender kit on the flange that sits atop the drain, raising the level of the flange to the level of the new floor. Secure the extenders to the flange with the provided screws and a screwdriver. Run a bead of silicone caulk around the perimeter of the flange.
Reinstall the toilet, using the reverse steps that you took to remove it.
This is a good time to replace the wax ring that seals the toilet to the drain.