What is the best way to backup files from my installation?
The best way is to contact your host and request that they set up a backup routine via crontab. How often will be up to you but you'll want to back up the following items/areas:
A) The database. This is probably the most important thing to backup. Your host can set a routine to backup once a week or more often if you like.
B) Your templates areas: /cms_admin/phptemplate/* again your host can create a cron to automate the backups once a week.
C) Your area files. The files inside your members and tour folders. This can be less frequent as they typically do not change as frequently
The concept with backups is that if something happens to your server(hacked, disk drive fails) that you have something to go back to in case of a catastrophic failure. How far back is determined by how often your backups are scheduled. If you have backups every week, then you've only lost at maximum 7 days worth of work and changes. If you have monthly backups you've lost a month's work of work and changes. How often should reflect how comfortable you are redoing work. Catastrophic failures ar rare but when they happen you lose everything if you don't have backups.
It is a good idea to download the backups to a local disk or make sure your host backs them up to a location separate from your server.
Your host is your friend. Ask them for advice on a schedule and what are best practices for backups.