ok, this is something i've been working over.. The hexing for awhile..
Ok 1st thing is you need to download the right Hex
Then install flip 3.4.2 (google is your friend for finding it)
Then plug the usb dongle in, will need to plug & unplug 3-4 times, till both red & blue led shows up.
then goto devices in Flip, select ATMega32U2
Then file / load hex
then settings, communications / usb
it then should connect to your AVR
then bottom left, click the run button..
This should then flash the hex onto your AVR USB