How to separate applications from data

I have read that it is very helpful to separate the applications programs on one disk or volume and place the data on a separate disk or volume..., as described below :

"Avoid putting your data (images, spreadsheets, documents, music) on the same volume as your system, and preferably not even on the same physical drive as your system (eg a partition on the same drive as the system). It’s one thing for a hard drive to fail; it’s quite another to have both the system and your data gone." This is from the diglloyd.com website.

My system has multiple hard drives, but this newbie is wondering how actually I accompany this..... do I simply save the photos, spreadsheets , etc , onto the different drive as I am working with them within the applications?

Please withhold your snickers....I have heard there is no such thing as a dumb question, but don't want to be the first person guilty of asking one....