I was wondering if you had an mega 2560 just the chip and connected the vital pins to an arduino uno, would you be able to upload to it? I was wondering this because I notice that the arduino uno and arduino mega 2560 boards are alike.
Sure, just remove the 328p chip from it's socket on Uno board and add four wires from the uno board to your 'standalone' 2560 based board, pins 0,1, reset, and a ground wire. You are effectively just using the Uno board for it's on-board USB serial converter chip and even the auto-reset should function to support IDE uploading to your standalone board. First you will have to get a bootloader burned into the 2560 chip, but even that is possible if you have a uno board loaded with the arduinoISP sketch and the proper wires to the 2560 'target' chip.