I know the above was posted last month, but I got that same light bulb a few days ago as my brain was assuming the same things you were. I kept skimming over display lists looking for a 'how to set the graphics mode' in the same book hehe.
I've pretty much picked up the basics from 'Atari Roots - A guide to Atari assembly language' http://www.atariarchives.org/roots/
and De Re Atari http://www.atariarchives.org/dere/ (Although still going through this)