Ubuntu is awesome, I use regular old Ubuntu myself. I don't know much about Xubuntu itself (i've been using Linux for quite awhile), but i'll assume it's good.
Manually backing up a XOOPS site can be as simple as you want it to be:
First, I always compress the files for my site using the tar command (Apache is setup to serve files from the public_html directory on my server, your mileage may very)
for example, if i had a site called MYSITE, located in the directory /home/MYSITE/public_html/ I would enter:
tar cfvz MYSITE.tar.gz /home/MYSITE/public_html/*
that would create the file MYSITE.tar.gz, which you can copy somewhere (more) secure.
Next, I dump the MySQL database tables. This just takes all the stuff stored in the database and dumps it in a file, so that it can be put back in. Depending on the way MySQL is setup on your machine, you might need to enter the password. This is the command, with the MySQL username being MYUSER, and the database containing the tables for my site is called MYDATABASE:
mysqldump -u MYUSER MYDATABASE > MYDATABASE.sql
This creates the file MYDATABASE.sql - which you should put in the same place as the rest of your backup (the MYSITE.tar.gz from above). **if you need a password in your MySQL setup, the command looks like this:
mysqldump -u MYUSER -p MYDATABASE.sql
That's pretty much it - anything else is just extra to make it either easier, faster, or more secure. Doing this, and sending it to another machine (or burning it to a cd, putting it on a thumbdrive) will keep you pretty safe.
As for how often to backup, I always judge by how often the content on the site changes - you obviously don't need to backup a site once an hour if it only gets 10 posts a day, but if it gets a lot of posts and contains things like development type work, I would backup as much as I possibly could in regards to the system overhead (you don't want your site to be slow because of constant backups.)
*btw - tarring it wouldn't work for a high traffic site, at least not very well, it would be much faster and a ton more efficiant to use the Linux rsync command, but we can cross that bridge when we get to it.
good luck, hope it works out!*/