I agree that the setup out of the box can be confusing. Forums and Groups are interconnected. A Forum contains the information that people discuss. A Group contains the people who are discussing.
When we launched a Buddypress site for the American Association of Independent Music last year – http://a2im.org/ – we had to write our own plugins to have groups work the way the Association wanted them to work. For example, Committee members belong to a group for that Committee and we did not want anyone commenting about a Committee to then automatically become a member of that Committee. A lot of the site is private for dues paying members, but you can see a slide show here: http://bit.ly/cV7CIF