well, auto-tools has 3 functions, auto-label, auto-move and auto-watch
for now, we'll talk about just auto-label and auto-move
let's say your download dir is /home/user/download/
with auto-label, you create a bunch of dir's in this path, so if you wanted to sort them by tracker, you'd do something like this:
/home/user/download/Tracker1/
/home/user/download/Tracker2/
/home/user/download/Tracker3/
and maybe even
/home/user/download/Tracker1/Movies/
/home/user/download/Tracker1/TV/
whatever....
so then, if you pick one of those sub dirs as your download path, auto-label will make a label with the dir's name, so forinstance, if you set a torrent to download to /home/user/download/Tracker1/ it will have a label of Tracker1
Then, if you set up an auto-move dir, it will replicate the same dir structure in another spot, so for instance, let's say you want all complete torrents to replicate this structure in /mnt/p2p/
a torrent added to /home/user/download/Tracker1/ will download, then when it is finished downloading, it will be moved to /mnt/p2p/Tracker1
at which point, it will seed from this new location.
This can be very nice for manual downloading but even nicer for RSS because you can automatically download and sort stuff, and it will only reach a destination dir when it is complete. I also use this method on a seedbox in conjunction with rsync, that way you sync data from one location to another. It can be very nice.