I’m working on laying out my first PCB, for the sake of learning how to do it.
I’m using Eagle for my layout.
I want to bring in an arduino board on completely separate layers from my actual board layout so that I can reference it to make sure that everything lines up correctly.
You don’t have to put it on different layers to reference it. Just add a shield in your schematic, in the board view, move to where you want, place your permanent parts over it, then delete it from the schematic. Done.
You didn’t specify what Arduino you have, so can’t help that much… Another thing you can do if you have an UNO, just use Sparkfun’s shield. There is no need to reinvent the wheel… You can use this method if you are making a shield for the UNO.
I’m pretty sure that the Adafruit Eagle library has an arduino shield component. Simply add it to your circuit, and it’s package is the shape of an Arduino shield, with the connectors already placed.