One of my latest screen prints, 4 colors on wood panel. I used a pen drawing on white paper, scanned it into Photoshop, and separated each color to its own layers. Photoshop is very similar to screen printing in the way layers work, and it is a helpful tool in determining layout. I often turn up the transparency of layers in Photoshop to see the trapping (small overlapping of stencils to prevent those weird edges where the screens are misaligned) and to work out overlapping transparent colors on the final print.
Once all the layers are done, I color everything 100% black and print each layer onto a transparency. If you are using registration marks, you can have those on their own layer and leave them turned on for each transparency, ensuring they are all in exactly the same spot.