Hi jolouis:
The 3V&5V PINs is simply a psthrough from the main 3.3V and 5V.And the 3.3V is the power of system,you need to be careful if you want to connect extra part.
Default means the PIN must be 0/1 when the device power up.(GPIO0 is 0 on our board).
Our domino Core Pinout show clearly of how it shoud be.Please reference it.
Thanks