APM 2.5+ Bootloaders

In both the interest of saving money and learning how the ATmega32u2 is used as a makeshift FTDI chip/PPM encoder, I plan to make my own APM 2.5+ using the open source Eagle files.  The only hurdle I foresee is burning bootloaders on to the ATmega2650 and the ATmega32u2.

I have used the arduino as an ISP to burn a bootloader on an ATmega328P, so I would prefer this method because it is cheap and well documented.  However from what I understand the APM 2.5+ has a different bootloader for the 2650 than what the IDE provides.  How can I burn this new bootloader while still using an arduino as an ISP?

Next, the ATmega32u2 has a DFU bootloader on the APM 2.5+.  I see it is provided in the google code repository.  https://code.google.com/p/ardupilot-mega/  How do I burn the bootloader using an Arduino as an ISP?

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