I'm supplying power to Arduino via PC USB.
Here's a block diagram of how the Arduino power is arranged:
As you can see the USB power is fed through a FET (P-channel MOSFET) to isolate it when there is external power applied (as decided by the comparator COMP). External power is fed through a 5V regulator and is fed to the same point as the USB power. Thus you get the same 5V at the same point regardless of if you have USB or Barrel Jack power. From there the 5V (wherever it comes from) is fed into a 3.3V regulator. The 5V pin on the Arduino is connected directly to the 5V point where the USB and the 5V regulated input are connected. The 3.3V pin is connected directly to the output of the 3.3V regulator.
So no matter what input power arrangement you use - barrel jack, USB power, battery connected to the V IN pin (not shown, but connects to the barrel jack), or regulated 5V into the 5V pin, you get access to the same 5V and 3.3V power on the 5V and 3.3V power pins.