The new firmware zip file has a tutorial in it.
Did your MP-D2 MKII come with the Arduino Board? You need one for flashing the Atmel chip in the MP-D2. Or you can flash a new Atmel chip and swap it with the Atmel in the MP-D2.
My MP-D2 didn't come with a new Atmel chip so I flashed the old one with the program XLoader. I am not sure if it erased the old flash first, it still worked. So I thought maybe I should try erase the old flash and I did that with the Arduino program. I believe when you run the Arduino program in order to erase the Atmel chip you just don't load a hex file. Then I flashed the Atmel chip with Xloader and the new hex file.
The Atmel chip has to go into the Arduino board the correct way or it wont read/write. I put the Atmel in the Arduino board the wrong way at first, just rotate the chip 180 degrees. When I took the Atmel out of the MP-D2 I marked the top with a red felt pen and I believe the top of the Atmel goes to the middle of the Arduino board.