I use the ArduinoDroid IDE on an Android tablet with a USB cable to a FTDI to upload sketches to a bread-boarded 328.
The 328 is powered by a 5v wall wart...that I unplug prior to uploading a new sketch.
Sometimes the tablet (via FTDI) is apparently unable to power the board and peripherals (SD card, LCD, and more...): the LCD goes black and the upload fails.
I'm thinking of leaving the wall wart plugged in during uploads, but first clipping the 5v pin on the FTDI header (so the two power sources won't fight). The power sources will share a common ground via the FTDI's ground pin.
I can't think of any reason why this shouldn't work or might cause problems.
Can you put a second header on the breadboard with the power pin missing?
That way you won't need to damage the FTDI connector.
On a board I made recently I put a little jumper that I can remove before I connect the Pro-Micro to the USB cable so that the external power supply no longer powers the Arduino.
I wasn't thinking of modding the FTDI itself. I have six pin (male) header attached to the breadboard; the FTDI (with female connectors) attaches to it. I was just going to snip (or bend) the power pin of the male header.
I forgot to say that another useful option is a header that does not have a Reset connection. That allows you to connect the FTDI cable and see what the Arduino is sending to the Serial Monitor without causing the Arduino to reset.