Here's a simple way to do that. Enable Libraries from Folder Options (if they're off) and then open the Properties of your Documents Library. Select the 'Documents' folder and click Remove. Now you have an empty Documents Library. You can add only the folders you want there using the Add button and completely ignore the "My Documents" folder.
If you use Winaero Tweaker:
http://winaero.com/comment.php?comment.news.1836, you can even remove the My Documents folder from "This PC" (via "Customize This PC folders" page).
You can also go to the "Customize Start Menu" tab in Classic Start Menu Settings. Double click the Documents item and set it to Documents Library. The rest of the junk will be in "My Documents" folder and you will never see it in Documents Library.