The Arduino Mega does have a 5V 1A power supply onboard that takes a 9-12V barrel plug type power supply. If you have both USB and the 9V-12V external power supply plugged in the Arduino will automaticly use the external supply for power instead the USB.
There are 3 different versions of the Arduino Mega 2560 that have different chips for USB communication: - the old official design with a FTDI chip - the new official design with an ATMEGA16U2 - and an unofficial chinese redesign with a CH340
The unofficial chinese redesign is the cheapest but since you can also get a clone following the official design for about ~$10 (like ebay #360790082588) I would just buy that instead. Especially since all shields and cases are designed with the official design in mind.
As soon as I have received the pcbs and can confirm that I didn't mess up, I'll post the Eagle files.