First of all you need to wire up your keyboard as described here and upload the skecth after you downloaded requirements which is described in project  GitHub page. 

After that should reset your microcontroller EEPROM or disable read EEPROM function before adjusting, to do this you can uncomment clearEEPROM() or readEEPROM() comment and upload it into your Microcontroller. After, you can send your adjustments by using application. When bindings uploaded you can uncomment readEEPROM or comment clearEEPROM() function and upload skecth again. 

All instruction above there maybe useless but if you faced with a problem this should be work. Still you have some problems about keyboard there some points that worth to check:

1) Data transmission between microcontroller and PC: 

This problems becomes different ways. They are probably comes from:

a) Encoding Errors: When you send data to your microcontroller, encoding problems can be happen. I solve this problem change the encodings if you faced same problem too you can try to do this solution. When you push a button and it press bindings that you do not adjust it can be happen from here because it might be ignore your adjustment keys or show an error message.

b) Transmission buffer problems: Project uses a method like handshaking because serial buffer sometimes misses value if you do not wait enough. If you want to increase transmission speed you can be face with this problem.

2) EEPROM's status: 

As it is discussed above you can reset your EEPROM if you have some issues.

3) Restart your keyboard: 

Sometimes all your problems can be solved unplug you keyboard and plug back in different port. 

Note: If you are facing a problem like opening port on the computer. You can solve this by closing serial monitors that opened in programs.