Atmel Flip and TKG are merely tools used to flash firmwares. It doesn't matter if you used EasyAVR or TKG or TMK to build your firmware, Flip and TKG can flash it. I just spent 20 minutes writing a nice guide but then I pressed refresh because I'm a serial refresher and it's all gone. I'll write a quicky.
1.
BUILD YOUR FIRMWARE WITH WHATEVER. This should produce a '.hex' file.
How to get drivers and use Flip1.
Download it and install (it requires java).
2. Plug in the board you want to flash
3. Put it in bootloader mode by pressing the button. You should hear the device disconnect sound.
4. Open device manager and look for Universal Serial Bus Devices
5. You should see atm32u4DFU or atm32u4 possibly with a yellow exclamation sign.
6. Right click > Update or Install Device Drivers > Browse my computer for drivers
7. Check the Include Subfolders box and brows for your atmel flip install folder.
8. Hit next. This should install atmel flip drivers.
9. Follow this video guide on how to use flip: Not a valid vimeo URL - your board has to be in bootloader mode to flash.
How to get drivers and use TKG1.
Download and install zadig This is what will find the right driver that TKG is expecting.
2. Put your board in bootloader mode
3. Open zadig 2.2
4. Now follow HPE1000
So moistgun helped me with that same issue when using TGK. You have to put the board in bootloader, then launch the exe in the tool folder called zadig. Go to options, show all devices. Then choose this option
Show Image
Then you do the setup.bat file
choose
2
N
1
1
then drag your keymap.eep file onto the reflash.bat file and follow directions
That should do it.