Like i said, I don't have one of these boards, so I'm going on what I can find on the website.
Take a look at the schematic: http://www.ladyada.net/media/boarduino/ ... inosch.png
There's a jumper labeled PWR between the 5v pin and VCC. If that jumper is attached, then the 5v pin and VCC are connected.
In that case, you can think of the 5v pin as a just a piece of wire. It's not an input or output, it's just wire connected to VCC. You can attach a power supply to that pin, and everything will work because the wire will have power. If the wire gets it's power from USB, it's still just a wire with power.
Does that make sense? I suggest you just try connecting your 5v power supply to the 5v pin and see if it works.