If you're talking about just understanding the OS itself and shell scripting I suggest you read the tutorials that come with your Linux distribution. The Ubuntu and DebIan guides cover the basics through very advanced concepts.
A good book that covers everything from the hardware and number systems on up is available as a free PDF all over the web and is called: LINUX: Rute User’s Tutorial and Exposition. It's from 2001 but it's still valid for learning the basics of Unix/Linux. It's very thorough and not a bad read.