You can tell the bootloader is active when the red 'Boot' LED pulses/breathes The board will then show up as a Serial or COM port, and you can use avrdude to program it. The 'programmer name' is avr109 so for example, to test you should run avrdude -p m32u4 -P COM3 -c avr109 which will initialize the bootloader.
You can find the serial port COM# in the Device driver, or for mac/linux users run ls /dev/cu.usb* to list all usb serial devices
The bootloader will time out eventually (after about 10 seconds) Because we are not using a USB/serial converter, bootloading is tremendously fast, we can program a full chip in under 2 seconds!
The bootloader takes up the last 4K of FLASH, so be aware that you will only have 28K instead of 32K. We have found that this isn't very constricting as 28K is still plenty. If you'd like more space, you can always use the 6-pin ISP connector and an AVR programmer (which will delete the bootloader)
If you ever want to disable the bootloader you can cut the bottom 'HWB' jumper trace. This will disconnect the 'hardware bootloader' pin, you can then use the button as a plain reset button. For the first few runs of this board we set the fuses to still use the bootloader even with the HWB jumper cut, if you want to get rid of the bootloader, please set the fuses to remove the BOOTRST fuse. Sorry!