How do I design a circuit to allow for two power supplies of the same voltage?
You can try the same scheme as used on and Arduino Uno. Sense the power supply voltage using a voltage divider and an op-amp. If it lower than your threshold, connect the board power to the FTDI's power via a p-channel MOSFET.
See the circuit in the top left side in this schematic, consisting of RN1A, RN1B, U1A, U1B and T1.
I hope you can get an idea of how to build a circuit for your application. If you can't come up with an exact circuit, I can edit this post to include a custom schematic for your application.