After you make sure power/ground aren't shorted, make sure that any silk screen or pin 1 markings for polarized components are correct - you don't want to go soldering that kind of stuff in backwards. After that it's really kind of random.
I was involved in bringing up a number of multi-layer boards over the years (not my designs) and we had pretty much any kind of screw-up you could make - traces that didn't go where they should, traces that simply weren't there, pads that weren't connected to their traces, etc, etc. I once even saw an issue where a broken trace was caused by the guys who built up the board gripping it wrong with pliers to break off a break-away section.
We were doing high layer-count designs, so we also had a lot of internal layer foolishness that you aren't going to see on a 2 or 4 layer board (registration can be...interesting when you've got 10 or more layers).
Once you get past the power/ground thing, you're probably not going to have too much trouble. Just take your time, test each bit of functionality one by one, and you should be good to go. If you're feeling paranoid, you could try building up the board one bit at a time (first put on and test the power, then the CPU and it's communications.
If you're feeling REALLY paranoid, you can sit down with the schematic and a meter and buzz-out the entire board. But unless the board is really small, that's gonna take a while.
You definitely want to get the main board working before you start on the secondary boards.
Good luck!
Generic pin headers are in the "pinhead" library. For something like the breakout board with multiple rows of headers, you can just place them in the proper locations on the board layout.
That said, do you even need to create a PCB? Since everything is on .100 inch centers, you could just get a protoboard, and solder your connectors on with point-to-point wiring.
If you want to go to the trouble and expense of making a proper PCB, you may want to consider starting from the Fio design files and integrating the motor driver on-board. The connections will be more secure, and you will save the mass of the extra PCB.
Best Answer
Autosplice (and possibly others) make solderless teminals like these:
See the datasheet here. These can be pressed into the PCB with some gentle force if you don't have too many pins to connect at one time. You'll need to solder the straight end into the main PCB.
Note that neither these headers nor the PCBs you press them into will have high cycle counts - The headers will flatten, and the hole plating on the daughter cards will be gouged by the headers. Note also that the connection won't be as durable as a soldered link; don't subject these to lots of vibration or tension from a cable connection. If either of these problems are a showstopper, you'll need a standard connector with a soldered link.
However, for your "In case they fail" application, this should be a fine solution. Sparkfun is out of stock, you can email the manufacturer at sales@autosplice.com or look at their distributors.