The books “Agile Web Development with Rails” and “The Rails Way” are both pretty good. “Pro Active Record” goes really in depth for Active Record, but doesn’t touch on too much else. The podcast Railscasts sometimes just uses the magic, but sometimes it explains what is really going on. Various blogs such as Art of Mission can get into what your looking for.
Additionally, using the ruby-debug gem gives you a much better understanding of what is going on – you can step into what is running behind the scenes.