The tracking ID simply partitions your sales statistics. How you use it is down to you.
You don't "add" the tracking ID, you decide which tracking ID you want when you first create the link or widget code within your Amazon account. To retrofit a new tracking ID you will need to create new codes replace the existing Amazon links and widgets on your site.
If you are usng multiple tracking IDs on the same site there is always a risk of getting them mixed up if you use an old page as a template for a new one in a different section.
Before anybody jumps in to correct me I know that you can retrofit tracking IDs if you know your way around html but the tone of OzJackson's post suggests that either he is not comfortable with doing thast or that there is some issue about his particular hosting account that makes this difficult.