You've got the right idea, but it's upside down. The rubber membrane goes underneath the mortar bed. The tile goes directly on the mortar.
If you have a tile store in your area (like Tile Source or Color Tile), they often will have a demonstration set up on site that can answer your questions (you can usually buy the appropriate materials from them as well).
A while back, Moderator Steve, did a very nice piece on installing the rubber membrane in a shower enclosure. You might find it helpful. Put his name in the Search Fix It For 'Em text box at the top of the screen, and set the In box for User Name (put in Moderator Steve).