If you build the controller by yourself you need to flash the firmware after the board is assembled.
Use an ATMEL programming tool, set it to ATxMEGA 128 A4U
and flash THIS hex file.
No other setting is required, after flashing was completed sucessfully you can test the board.
Prepare the board for the TFT Display:
There is a jumper on the board which sets the display mode. Solder a bridge as shown in this picture:
Connect the display as described HERE (this is a German manual, but you need to see the pictures only).
Apply +12V to the board (check current, should be < 0,1A)
Switch the board ON by making a short connection (i.e. with a push button) between the pads ONOFF and GND.