ATmega2560 bootloader to use more i/o pins

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  1. Yes indeed. The MKii is pretty versatile. I have never locked up a chip using it and the Arduino standard fuse settings.
  2. If the bootload failed, just load it again.
  3. Yes, use the Ardiuno bootloader.
  4. Yes, you tell Atmel Studio what file you want to load into the boot flash space.
  5. Yes, uploading a sketch via ISCP wipes out the bootloader - but the fuses do not change. Using the bootloader to load via the Serial interface does not affect the bootloader.
  6. As long as you have an ICSP header and a serial header, you should have a lot of flexibility program loading wise.