Should I disconnect the FTDI and ICSP power supply pins via a device like the NDT2955 every time the on-board power supply is also supplying power?
Simply don't wire the USB +5vdc power from the connector/FTDI chip to your board, just the ground and signal lines. Then you can always use your external power source regardless if you are plugging into the FTDI signals or not. It's never a good engineering practice to hardwire two +5vdc sources together and that is the purpose of the arduino's auto-voltage switching circuit. On much older Arduino USB boards they just used a simple three pin selector clip to manual switch between USB power or +5vdc from the on-board +5vdc regulator, a simpler and to my mind more elegant solution.