I think that when you set iTunes to "manage files manually", you can actually simply dran and drop files from any folder (I am assuming you use windows) into the iPod, without bothering having to deal with iTunes music collection.
Also, in "manage files manually", iPod content becomes "editable" directly, again without any need of the Music Collection section of iTunes. Any change you make to those files (tags, etc) will be made into the iPod itself. The only problem I found is that, if you use your iPod this way, you won't get any album art into it.