I mark the centers of the backing and batting and top before starting to layer. For batting, I use a Sharpie permanent marker (will not bleed later). For the backing and top I usually just fold in half and iron the crease. Otherwise I do mostly as Lisa wrote, except i do not clamp down the batting.
It's really important to position two layers first, then fold whatever is on top halfway down before glueing. I forgot to do that once -- laid out the backing, sprayed the entire backing, then struggled to position the batting on top of all. Ridiculously difficult! Don't spray (or glue) until you have two layers positioned correctly, then fold down half of the top layer before spraying (or spreading glue) so you are doing only half at a time.