Hand screen printing is typically a one color method of printing. But there are ways you can incorporate multiple colors without dealing with multiple screens and registration marks. One way is to blend colors on the screen as you are printing. Another is to have 2 screens - a positive and a negative, for instance the outline of an object and the interior on a separate screen. Another way I've found to incorporate color is to print in black on a colored fabric. I then apply a fusible product, either Pellon Wonder Under or Misty Fuse to the back of the printed fabric, cut out the print (retaining the black outline) and fuse it to the quilt. Here are some examples.
The bird was printed on the purple, cut out and fused, and quilted.
This butterfly has been used in a few pieces.
These black-eyed Susans are destined for a new project. You'll notice that they are cut into individual squares. That was done on purpose to make the printing easier. I don't like to waste fabric and wanted to print close together, but I didn't want to get paint on the back of the screen. It was quicker and easier to print on individual pieces. After printing, I applied the fusible to the back of the squares and then cut them out. Then they're ready to fuse to your project.