I had trouble with that at first too. I'm no expert but it seems that the main list (the All list) is everything the DB scans for, on all accessible satellites, in one huge list. What you work with from day to day is the Favourites list, and what's in there is what you put in there, from the main (All) list.( However, I don't know if renaming them is possible anywhere.) It's a good system, because it lets you work with a manageable channel list, more so if you've enabled Bouquets so you can subdivide the Favourites list.

Hope this helps.