Welcome to the Parallax Discussion Forums, sign-up to participate.
The STOP button will be terminated to one of the two pin headers for E-Stop and over-travel, which goes to IO pin P3 of the Proto Board.
I will be exposing and etching two new boards tomorrow, one for the user interface and the other for the power supply switcher.
You know you have it just right when you pull it out of the developer and all you see is highly defined traces, pads, and holes.
Good luck, and I'm hoping your double sided circuit board adventure will work.