Well, actually, some trackers don't associate with the passkey, so you weren't entirely wrong. For those trackers that use your Browsing IP, you will have a problem unless you configure rTorrent to announce your home IP (insecure). But for anything else, just download and throw it up on FTP into your watch folder.
Use ssh in terminal to manage the box. Read up on root/sudo and the rm command so you know how to clean up after yourself properly.
If you have basic questions, feel free to pm me, since I run a a linux seedbox through my Mac.
Bookmarks