Zen uses QMK firmware. Documentation on installation, keymaps and compiling can be found here.
If QMK Toolbox doesn't work, try these steps
To install the default keymap:
Download the left/right eeprom files and .hex files here
Right-click each link and "Save link as..." or download the whole repo
Flash the left half
For Elite-C choose
FLIP USB DFU protocol version 1 (doc7618)
For Pro-Micro choose
Atmel AppNote AVR109 Boot Loader
Flash: choose your hex file
Press the reset button or short RST to GND
Flash the right half, but use
Plug the leftmost port into your PC, and the two middle ports into each other.
After the initial setup, you can update your keymap using QMK Toolbox, and you only need to flash the master half.
For custom layouts:
Follow these steps
Install and setup QMK and Avrdudess
Edit your keymap as desired and compile hex file
Flash the hex to the master (follow guide above)