Let's see if I get this straight: you want to connect over USB (for serial communication) but you also want to power the Arduino from an external 5V power supply connected to the +5V output pin. Right?
I doubt there will be a massive current loop anywhere because a) there is a 500mA PTC in series with the USBVCC power supply, and b) internal wiring resistance on the PCB traces will serve to cause current load sharing between the two supplies.
It's still not the greatest idea IMHO as if your external supply decides to go rogue (or your hand slips on the voltage knob) and climbs up to 6V, 7V, whatever then you could damage the USB port on your computer (Method #5 of destroying your Arduino).
I'd consider going with an external 7V supply and using the DC power jack.
--
The Basic Motor Driver: simple, inexpensive motor driver for 1 stepper motor or 2 DC motors