Changing bootloader fuses - Arduino based ATmega32U4
The program to use would be avrdude. 

What you need to change is not so much the bootloader (although if you want to build an Arduino compatible board, you'll need to upload an Arduino compatible bootloader) as the fuse bits. 

The details of those (e.g. clock rate, brown out settings) are generally not relevant for Arduino compatibility, but the cleanest approach is to make a custom entry in boards.txt for your board, cloning e.g. a Leonardo entry but tweaking the fuse bits to your preferences. That allows you to set those fuse bits through the "Burn Bootloader" command in Arduino.