I have finally got it working absolutely fine.
For anyone else that might need it, see this below.
Install RTorrent via:
Copy and paste this into /home/<username>/.rtorrent.rc replacing <username> with your current username or the user you wish to download torrents with:
sudo apt-get install rtorrent
directory = /home/<username>/Torrents/Unfinished
session = /home/<username>/.rtorrentsession
schedule = watch_directory,10,10,load_start=/home/<username>/Torrents/Torrents/*.torrent
schedule = tied_directory,10,10,start_tied=
schedule = untied_directory,10,10,close_untied=
on_finished = rm_torrent,"execute=rm,$d.get_tied_to_file="
on_finished = move_complete,"execute=mv,-u,$d.get_base_path=,/home/<username>/Torrents/Finished/ ;d.set_directory=/home/<username>/Torrents/Finished/"
schedule = low_diskspace,5,60,close_low_diskspace=1000M
schedule = ratio,60,60,"stop_on_ratio=100"
check_hash = yes
This assumes you have the folders:
If you do not have these folders, make them now using "mkdir" or simply make them using a GUI.
What this configuration does is check the folder "/home/<username>/Torrents/Torrents" for new .torrent files and starts them automatically and stops them if they are removed. Once the torrent has finished it is automatically moved to the Finished folder. If the torrent is still active it is found inside Unfinished. It is also set to use Encryption if it can, as this will hopefully navigate some of those nasty ISP who shape their bittorrent traffic.
You can now run this from a terminal by running simply "rtorrent". However, to make this only start at certain times, in my case 4am until 4pm, you need to do this:
Install "Screen" if you havn't got it already. Desktop Ubuntu does by default but Server users may need to install it:
Now you need to edit your crontab. You can do this by typing this at a terminal:
sudo apt-get install screen
Copy and paste this into it:
The bits in bold are the hours in the 24 hour clock. The bits before that are the minutes. Simply change these to the times that suit your needs.
# m h dom mon dow command
00 04 * * * screen -d -m rtorrent
00 16 * * * screen -r -X quit
What this does is start rtorrent in a "detached" screen session. Then, at 4pm, it makes screen quit any detached session. Thus giving you the desired effect.
I hope this helps someone as i've been stubling around for weeks now.