Bryan Siepert has published a new Adafruit guide on creating custom circuit boards with EAGLE:

Make your own PCB with Eagle, OSH Park, and Adafruit!

This guide will introduce you to the basic process I use to build PCBs based on Adafruit and other open source designs. We will extract parts of the board files as what Eagle calls “Design Blocks” and then we will use them along with a fundamental workflow in Eagle to create a featherwing-like board for the Trinket M0. This board will allow you to securely attach the Adafruit INA219 current sensor breakout to a Trinket without having to use jumper wires to connect them together. We’re starting with this modest goal to keep things simple as we learn some fundamental concepts, while hopefully also ending up with a useful circuit.

This guide will cover using a Trinket M0 and INA219 breakout, however these same methods can be used to make a PCB to replace the breadboard or protoboard. These techniques can be used to extract useful pieces from open source boards to use in your own completely new circuit boards.