I have a code for Extreme Tracking to add to my site. After enter the code into the HTML window and click on "OK", can I just upload or do I have to use "add files" ? If "add files" where do I browse to find the files I need to add to my root directory?

I assume that in the code that you inserted as snipped in VSD contains links to files outside the scope of your site.

I guess from this point on you have nothing more to do than just upload.
(unless certain file are required in your root which should be provided by Extreme Tracking)

It would help if you provide us with the code.

The code for Extreme Tracking does not require any files to be uploaded. It's just an HTML code that you copy and past where you want it too appear on your homepage. They host the tracking button on their own server so you don't have to upload it.

Open the Visual Site Designer, click the 5th button down on the left for the HTML Tool. It looks like a computer monitor with matrix coding on it. Drag a square where you want the button for the tracker to appear. When you let go, a box will appear for you to enter the HTML code. Place it under the "Body HTML" tab and click OK.

When you preview you should now see your tracker.