This might be obvious for you but as an electronics noob it took me a while to figure out how to connect the Sparkfun FTDI Basic Breakout board to the ArduPilot. The different naming of the pins confused me and of course I thought I'd blow up everything if I connect it the wrong way.

ArduPilot pins
GND = Ground
VCC = Voltage of the Common Collector
GRN/DTR (green) = Autoreset
TXO = Output
RXI = Input
VCC = Voltage of the Common Collector
CTS = Clear To Send
BLK/GND (black) = Ground

FTDI board pins (-> ArduPilot)
GRN/DTR -> GRN
RXI -> TXO
TXO -> RXI
5V -> VCC (unused)
CTS -> CTS (unused)
GND -> BLK/GND