I've been working through the great information in the thread concerning the configuration for this gadget, specifically the detailed walkthrough given by oneproduct. Using that, I performed a quick test to change my caps lock to a Ctrl and flash it to the device. Great!
Then, craving layers, I grabbed the TMK stuff from github and after reading the tutorial and poking through the makefile, attempted to load it with doubleshift-break for the bootloader, followed by "make flip" to deploy. This also worked! I'm typing on the keyboard now flashed with TMK.
I then went through and designed my second layer, however now I run into a problem--the keyboard isn't recognized as an ATmega32U4 anymore. I can't open up the device in FLIP, nor deploy. Is there a detail that I've missed somewhere?