It is my understanding, that you want to communicate with PSoC4 Pioneer Board using USB-UART bridge, built into PSoC5 programmer. For example, like this
Here PSoC4 UART Tx pin 0.5 is connected to PSoC5 Rx pin 12.6 using an external wire. It is my guess that the wire prevents using an Arduino-style external shield, which you would like to attach on top of the Pioneer Board.
In such case I would recommend to plug the shield, and to solder Tx/Rx wires at the back of the Pioneer Board. For PSoC4 Tx and Rx pins you need to select any pins that are not used by the shield.
PS. The drawing above was made using free librarie