CooperRamaCurrently, yes. It does not know how to write into the EEPROM. If you want a default mode, you can set it manually with compiling your own firmware.
CooperRamaDepends on what you need. If you want the default layout with the programs being switched around, then I can probably compile you a firmware for you. If you are comfortable with light programming you can follow this guide:
https://www.massdrop.com/talk/9382/how-to-configure-your-ctrl-keyboard
The code can be found here:
https://github.com/qmk/qmk_firmware
From there you're looking to edit files inside keyboards/massdrop/ctrl/
For sensible eeprom support there is ongoing discussion how to do that, because there are some caveats that have to be solved.