I suspect that sources like W3Schools, the O'Reilly Missing Manual series and DirectXTutorial.com leave out good practices to avoid overwhelming the reader.
This idea is sometimes called Wittgenstein's ladder: http://en.wikipedia.org/wiki/Lie-to-children - "My propositions serve as elucidations in the following way: anyone who understands me eventually recognizes them as nonsensical, when he has used them - as steps - to climb beyond them. He must, so to speak, throw away the ladder after he has climbed up it."
It helps. Let's take the example of numbers. You begin learning as a child with 1, 2, 3... Everything is an integer and begins with one. Rapidly, you learn the notion of 0. And then at school, at some point, come the negative numbers. You have to "throw the ladder" that numbers are integer and begin with 1. You still know how to count, indeed in a more complex way.
Let's say you begin with markup, and just put the style as a tag to begin with. At some point, you know what a style does, but you have to throw the ladder that it has to be inside the markup, and externalize it to .css file.
This idea is sometimes called Wittgenstein's ladder: http://en.wikipedia.org/wiki/Lie-to-children - "My propositions serve as elucidations in the following way: anyone who understands me eventually recognizes them as nonsensical, when he has used them - as steps - to climb beyond them. He must, so to speak, throw away the ladder after he has climbed up it."