You use the outer port to communicate via Putty, and use the COM port that is not the one you use with Arduino programming. Note that you do have to use external power when communicating with Putty, not with Arduino. Once you bring up Putty, you have to hit enter a couple of times, don't forget that part.
If your board is working with the Arduino IDE, then the board is obviously working. I expect you will get there with it shortly!