I'm really unclear on what you want. If you have some sections (categories) and you want to add forums under them, you do so in Forums & Moderators > Add New Forum and select the category as the parent forum.
Hmmmm, I'm not really sure. I'm not sure if you would just remove a template or what. I suppose you can try commenting out the contents in that template and see what happens. To find the template - vboptions > General Settings > Add Template Name in HTML Comments > set to Yes . Then go back to your page and view the source code and you will see the name of the template called around your part of the code.