So, I'm trying to burn the Arduino Leo bootloader onto a ATmega32U4 that's on 3.3V and the internal 8MHz clock. Do I have to modify and rebuild the bootloader to set the fuses correctly, and can this be done with AVR Studio?
All of the references on doing this are dated. The folder structure for the Arduino IDE has changed. I've done it in the past with 5V 16MHz 32U4s using an Arduino as ISP, but never with the AVRISP mkII on the Arduino IDE.
On the good side, I do have it up and running with Atmel Studio.