How would you go about building a stand alone atmega 2560?

Using Arduino Microcontrollers
2

Just look at the datasheet for the TQFP-pinout ATmega640/1280/2560:

10: VCC
11: GND

30: Reset
31: VCC
32: GND
33: XTAL2
34: XTAL1

61: VCC
62: GND

80: VCC
81: GND

98: AREF
99: GND
100: AVCC