Bootloaders, Board Definitions and Fuses

I am building my own boards and have been using the Adafruit M0+ bootloader.

When you program a bootloader with Atmel Studio, do all of the correct fuses get set? Or, are the fuses set independently of the bootloader .hex file?

Independently.

OK, that's what I figured.

I was reading fuses from an existing part and burning them to new parts. But, I don't think I was preserving the settings from the original "read" to the subsequent "write".

Is there any way (in Atmel Studio 7) to load a set of fuse settings, or do I have to enter them one at a time down the list?

Is there any preferred bootloader for the M0+? I see most are based upon the Atmel SAM-BA?

Thanks,

John