Is the positive supply of Arduino USB port connected to 5V pin?
There are a lot of "Arduino-compatible" boards which are sold as "Arduino" labeled. The schematic is common in general, but can be different in details. You should investigate what do you have on you specific PCB yourself (or post detailed images of the both sides of the board here).
I think, 500 mA limit comes from two factors:

a) USB 2.0 specification (500 mA max);

b) Some of the "Arduino-compatible" boards have fuse on USB power line of the same 500 mA value (but your specific board may not have it). Or, let say, the diode which can handle 0,5 A only.
"Normally" when your device (Arduino board + additional modules etc.) does some useful job you should power it from one definite source - USB or power supply. And you have to decide yourself how to power it correctly. Also powering from USB can be made from computer USB port or from power supply with USB output. The choice is up to you.


You can also unsolder fuse or diode from you PCB and then you'll get (almost) no limits to power current from USB input (but you'll get the risk of frying you USB port also, if something goes wrong on the PCB side).