Powering with ESCs and FTDI Cable during setup?

[Alterscape]

I'm working on building my first MultiWii copter using a BobsQuads Super Simple Shield, an Arduino Pro Mini, and a Genuine WMP board. I do not have the matching Bluetooth adapter that blueskyrc sells; I do have a Sparkfun BlueSMiRF I could set up if I have to, but I'd rather not for now. I noticed that the 5v rail on the Simple Shield is not powered when I power the Arduino Pro Mini over the FTDI USB-serial cable (and therefore I don't get any sensor readings). I don't have my quad in front of me right now so I could be making a silly error in memory, but I believe that's what was going on -- Is it safe to connect 5v in from an ESC's output (or a 5v bench supply, for now) to the board to power the sensors at the same time the FTDI cable is plugged in? I suppose to be extra safe I could not connect the vcc pin on the pro mini's FTDI header, but then I have to have the board powered externally whenever I'm flashing it, etc. Thoughts?

[kalle123]

I have two of those battery boxes laying around here for checking and testing my RC equipment.