You'll need to create backup scripts that tar (or zip) the directories you need, and then shoot them over to the backup space over ftp. You'll need to work out for yourself what to backup and how often to do it. You should'nt have to backup literally the entire server though. On mine I exclude a whole bunch of stuff, as an example:
tar -zcvf server.tar.gz --exclude=/home/fozl/server.tar.gz --exclude=/proc --exclude=/lost+found --exclude=/sys --exclude=/mnt --exclude=/dev --exclude=/media --exclude=/home/fozl/lolcats
Seems to work well enough.
You might also consider investing in a usb drive and just rsyncing your data to it, no need to concern yourself with network activity when the backup runs if you do that, you have your data nice and close and you get alot more space (500GB), and as you can use rsync (or just cp if you want) you don't need alot of working space held aside just to do the tar'ing iykwim. Does add to overall cost though.
http://www.ovh.co.uk/items/usb_disk.xml