Question : The pod is identified as "JTAG 3/5V" and in all of the documentation that I can find it shows the "PD" pin connected to Vcc. In the case of the C6X (w/ 2.5v core, 3.3v I/O) Should it be 3.3 or 5 Volts. Will this causes damage to the device/dsp if it is set to 5Volt ? 

Answer : The PD pin on the JTAG header is not connected to the DSP, so it will not cause damage to the DSP. It is only connected to the pod. It's purpose is to have an indication to the XDS that the cable is connected and the power is applied. Since the pod labeled 3/5V is tolerant of both voltages, having PD connected to 5V even though you are running a 3V device is no problem.