joshuab 
I had a four-hour flight today, so I spent some time playing around with DipTrace trying to figure out how to integrate the Boarduino PCB into my PCB. Finally, I figured it out. First, I opened the Boarduino schematic and pasted my schematic into it, then hooked up my components to the Boarduino schematic's pins in the appropriate ways. Next, I opened the Boarduino PCB file. The key step was to select and "lock" the Boarduino PCB before doing a back-annotation to the schematic. Before, when I back-annotated to the schematic, it would erase all of the Boarduino PCB's nice, professionally-designed routing. With the Boarduino locked, all of its routing remained, and my parts were added to the board with rat-lines, so I could finish routing them. This is a good step if I ever get to a point where I want to produce the boards on a larger scale. For one thing, it wastes none of my valuable PCB space. For another thing, I can order the components of a Boarduino from Mouser (qty. 1) for about $7, whereas they cost $18 from Adafruit. $5 of that $18 is the Boarduino PCB itself, which I'll no longer need.
Keeping the Boarduino layout is very desirable, as it includes a nice, regulated power supply, ICSP header for programming, and and all the other support miscellaneous that are needed.
