Yes you can use the turbo pcm, in which case you don't need to worry about the second knock sensor. Only bf onwards have 2 knock sensors. You will be better off using the 3 plug harness for the turbo pcm, if it is available to you. You can splice the boost control plug into a na harness if necessary. There is nothing that won't plug in, no matter which way you decide to go.
You will need to link the turbo pcm to the car, and possibly the trans if it has a zf. This can easily be done with Forscan, you can get a free trial of the extended licence to do this. I'll talk you through it when it's time.
Alternatively you can use the na pcm and just use a boost tee or electronic boost controller from GFB or Turbosmart etc.
After this and before you license the pcm for tuning, you will want to choose a suitable strategy for fully independent cam control, as the ba turbo pcms don't have that, unless it is a BA f6 pcm.