Hi Dillon,
To flash the bootloader, you'll need a PDI programmer. Some of the 3rd-party AVR programmers have PDI, some don't. Unfortunately, it looks like the programmer you picked up from sparkfun falls into the latter category. We use and recommend Atmel's AVRISP mkII. Note that while the AVR Dragon is capable of PDI, for some reason it does not support writing the bootloader section of the chip.
The command to flash the bootloader is
avrdude -p atxmega32a4 -P usb -c avrispmkII -U fuse2:w:0xBF:m -e -U boot:w:bootloader.hex
(you'll need to adjust the -c parameter if you're using a different programmer)
If it succeeds, you should see the LED blinking when you plug it into the USB port. This means it's in bootloader mode.
Thanks for noticing that I never finished the 'Firmware Hacking Guide'; I'll go post that.
--
Kevin Mehall
Nonolith Labs