I am just learning MultiSite WordPress myself. So far I’ve learned that if I want to edit Templates or Plugins pages for another site, I first have to activate the Theme I want to make changes to as my first level site, the Admin Site, or Edit the Plugin via the Admin site. Then, I go under the Main/Admin Site and edit the Templates or Plugin. After I have everything looking good, then I activate the Theme or Plugin for the actual site where I want to use the Template or Plugin. One must use this method (based on my learning) if one wants to use an external Editor, such as Dreamweaver.
I did notice that the access to the Activity, Sites, Forums, et al only show up in WordPress’s Tool Bar (the dark gray bar at the top of the page) under my Profile Link on the far right, when I am Logged In. I think this part is not clear in the directions, imo. After the initial install of BuddyPress MultiSite, I was able to see a couple of the BuddyPress pages links in the Main Menu of my top Site only after I am logged in.