TeslaIaint:
What you can do to help with conflict like when your standalone 328p and external circuitry is being powered up with a battery or other independent voltage source but the FTDI module is not plugged into the PC, is to use two series 1K ohm resistors in each of the Rx and Tx signals going to your standalone. That will prevent any 'back door' current flow in that situation.
Thanks Lefty. I previously just tried unplugging the 5v from the FTDI, but my "test power" led was still dimly lit. You say that a 1K resistor will work from RX of FTDI to TX of uC and another series 1K resistor from TX of FTDI to RX of uC while the FTDI is connected to the PC and the rest of the board is under external power? I just want to make sure I understand you.
Yes, that is correct. And by the way the standard arduino board design is to isolate the USB serial converter's send and rec lines with 1K ohm resistors. That is mostly so that it's somewhat possible to use pins 0 and 1 with user external components if not needing or using serial commands, but the isolation also works for having different or no power on the FTDI's module.
Lefty