While I don't have much documentation yet on the alignment procedure, here's some info about how I did it:
http://falconoutdoor.blogspot.com/2012/02/printing.html
http://www.chorca.com/wiki/index.php/Print_Head_Calibration
It can be frustrating, you need to have patience for it and a lot of print material. Make some movements to the head so you can get the feel for how moving things around affects the print output, and then start dialing them in.
It's not a fast process, I've used prolly 20ft of material just for calibration so far. Some was cheap vinyl, some was nicer inkjet stuff, but that's the price you pay to have an aligned machine.
The tough part is the mechanical bit; once you get the movements down and the heads locked in, the rest of the stuff is all just pressing buttons to move things about.