Pan uses QMK firmware. Documentation on installation, keymaps and compiling can be found here.
If QMK Toolbox doesn't work, try these steps
Choose ATmega32A in QMK Toolbox.
Choose the hex file to flash.
Choose a hex file based on your encoder and LED bypass configuration.
Hold the BOOT button, tap RESET, and release the BOOT button.
A device named "USBASP..." should show up.
Flash the board.
If your ATmega32A doesn't have a bootloader, you'll need to flash one using AVRdudess and an arduino
Make sure to download the bootloader hex here
Set MCU and fuses as indicated below
Wire up your arduino to the ISP pins located to the right of the MCU
Plug in your arduino to the PC and select the port
Program the ATmega32A