When you're working with bulky stuff, use something called transparent overlay registration. All you need is some acetate and tape. Before starting each new layer, place a piece of acetate on your printing surface. Tape down one side of it to make a hinge so you can flip the acetate on and off the printing area. Now make your first print with the acetate flipped ON the printing area. When you're ready to print on a tshirt, slide the shirt underneath the acetate and position the shirt using the acetate print as a guide. Once you've secured the shirt where you want it, flip the acetate OFF the printing area and print directly on the tshirt.
This gets more useful in the following layers. For each new layer remove the old acetate, attach a clean piece, and make your first print. Now when you position your shirt you can see through the clear parts to the previous colors and get really nice alignment (or purposeful misalignment, depending on your goals).
I wasn't printing tshirts, but I tried this for the first time on a set of holiday cards this past weekend. You can see pics (including a few of the acetate layer) here: http://www.flickr.com/photos/katy/sets/1414455/