Issue with flashing bootloader on APM 2.8

Hey guys,

due to some problems I have with the APM 2.8 (described here:Arducopter V2.8 after wrong wiring solid red LED and no connection to MP) I want to burn the Atmega 2560 Bootloader on the APM. I have a Arduino USB2Serial light/micro board of which I thought of using the ICSP port. I researched a bit and found out that I have to connect it with port 51-57 on the Atmega. It’s really unclear how the ports/pins of the APM are connected with the Atmega. Couldn’t find anywhere a layout or scheme of the APM 2.x Does anybody know about it??
It seems I can use the SPI on the right hand of A11 pin on the APM to connect with the Programmer. Is that true? Because when I connect, all LEDs on the APM are turning off immediately…
The question is how can I flash the Atmega 2560 on the APM 2.8 ?

Thanks a lot and greetings Sebastian