Breaking a sentence into grammatical structures There's a very robust deck of Anki flash cards I've been using to build vocabulary. But sometimes I get stuck when new grammatical constructs are shown.

The deck says 你想走的时候就走吧。 is translated "Go when you want, ok?" which clause is 时候 part of?
"Whenever you want to go, immediately go okay?" or "You want to go, whenever immediately go, okay?" 

Also, what resource(s) is best for building familiarity with these various transformations (or grammatical structures)? 

Thanks!
的时候 is an interesting way to construct time markers in Chinese, it means "when (something happens...)".

In your example, the whole 6 characters in 你想走的时候 are part of the ...的时候 construct, which matches your first translation, i.e. Whenever you wish to go, just go. or Anytime you want to go, just go. 

Well, the best resource to train your "parser" is just reading a lot, text books for the most part. And sometimes breaking up a sentence can be hard, that's normal, but the more experience you have, the better you will be at it.