Get the cheap bag of thinset, mix it with water and spread on the floor using a 1/4" square notch trowel. Set the cement board into the combed thinset and anchor it with backerboard screws or 1 & 1/4" galvanized roofing nails (much easier). Set at 6" around the perimeter, staying in a good inch from the edges, and every 8" in the body of the board. Cover the seams with mesh tape and coat with modified thinset (same that you will use to set the tile). Sand down any high spots after it dries.

The thinset under the cement board is only there to fill up voids and air pockets between the plywood and the cement board, the nails hold it in place.