Basic site structure/layout advice

Thanks to all. I just installed the faceted navigation plugin on my test site. I'll look into @espenmn's suggestion if faceted nav does not work.

Two things I noticed after I installed the plugin (I don't know if it's a coincidence or not):

  • I had edited the default homepage with my own content, but now I see it a new entry in navigation with the title of the page. No idea how or why this happended.
  • When I go to the site's main page and click "Content" on the admin sidebar, I used to see all my files and folders. Now I see nothing other than the word "Site" (See screenshot).

Anyone know what happened?