I'm not an expert on programming the ATMEGA32U4 with a bootloader, but I do know it uses the PDI programming interface, for which you need a PDI programmer. I doubt the ATMEGA2560 will do that, although possibly with a suitable programmer installed. You would need connections to PDI, PDO and SCK as described on page 361 of the datasheet. Then you need a suitable programming sequence.
I don't know where the bootloader file is. I presume it is on the Arduino code site somewhere.
http://code.google.com/p/arduino/
or, here maybe:
If that isn't it, someone else might know.