first youll need to make a board for your atmega 1280/1281 since it doesn't have a dip breadboard friendly version - buying the arduino mega pcb would be the best thing since the board has all the footprints to get the atmega working + a ICSP header
if your going to program the atmega via avr studio i dont think youll need the bootloader because all the programming will be done via the ICSP programmer
i also suggest that you get a dedicated programmer if you want to use avr studio - arduino as isp its a quick solution but not sure if it was intended to be used as a dedicated programmer