Ardueno PRO ports

I have an Arduino PRO. I see the six pin isp for programing. I assume I can use either a USBasp or a Usbisp on that port. I also see a six pin port (RST, TX, RX, VCC, GND, GND) for a FTDI programmer. I have not seen in Arduino program where I can define the FTDI port. What options do I have to set to use the FTDI port and why would I use one as opposed to the other?

The FTDI pins are connected to the hardware serial port on pins 0 and 1. Accessible from the sketch using Serial.

If the bootloader is present, you can upload code via serial - this is often convenient for debugging since you can easily use the serial monitor to read whatever your sketch is printing.