The boardcontroller and the Atmel ATmega1284P are connected together through TWI, SPI and USART. All interfaces can be used to communicate between the devices, but only the USART is implemented by default in the boardcontroller.
This represents the RX and TX on the Atmel ATmega1284P. The RX is connected to TX on the other device and visa versa
These signals can be disconnected from the boardcontroller by cutting the cut-straps marked SPI on the bottom side of the board