So let me start by saying that when we started the bathroom we did make mistakes. The first thing that we did was to tear up the vinyl floor that was down when we bought the house. That was a job that brought on instant sweat!
Then we bought Lauan board for $108.80, which was a mistake. We put it down only to have to take it up because it was too flimsy, and it wasn't the right sub floor for putting down ceramic tile. The tiles would have cracked under the pressure. So we returned five sheets of the Lauan board and got a refund of $49.87. So it cost us $59.83 for the sheets that we ruined.
First we put down Thinset, which is an adhesive/floor leveler compound. Then came the Backer Board. We screwed the backer board to the existing 1/2" plywood sub-floor. Be sure to sink the screws all the way in below the surface of the board so that your tiles sit flat. We started out using a hand tile cutter, but ended up taking that back to the store and got a wet saw, which was much easier and quicker for us to use.
After that we used the Thinset with joint tape for the seams in the Backer Board .
The next step, we used a white Thinset adhesive, with a trowel and spacers to lay the tile evenly on the floor.