Rtorrent is the torrent client itself. It resides on the server.
Putty is the program you use to access rtorrent's interface.
Utorrent has no role in the seedbox. This service is totally unrelated to our VPN.
Example of normal usage of the seedbox:
1) I go to a torrent site and see a torrent I want
2) I download the .torrent file onto my computer (not the file itself)
3) I use Filezilla FTP to upload the .torrent file into the seedbox's torrents folder
4) The seedbox detects this newly uploaded .torrent file and begins downloading the actual file.
5) You monitor your download/upload via Putty and access the rtorrent interface from there.
6) Once the file is complete on your seedbox, you download the file off FTP (Filezilla again).
7) Using Putty you remove the torrent (not the file) from your rtorrent after you are done seeding.
When you want to clear space, you use Filezilla to delete the file off your seedbox space.
Yes you can always use utorrent and the seedbox together to upload.
Bandwidth is limited yes but you can always choose to dl using both if you wish to.