If you can get your hands on it, Friedrich Heer wrote a primer on the HRE a long time ago that's fairly decent, if aging and kind of old-school in terms of style. I have heard that Peter Wilson, the author of a recent and very good (especially on Imperial politics and institutions) book on the Thirty Years' War, wrote another book about the HRE in history from the Reichsreform in the 15th and 16th centuries to its demise in 1806, but I haven't read it.
This is kind of a problem in German studies that's been only intermittently addressed over the years: there are very few up to date, in-depth books on the institutions of the Empire and the course of events in it as a whole. Most good books on German history over the last millennium look at the Empire and its politics as sort of peripheral to the main action, whether they are discussing the Hohenzollern monarchy, the Habsburgs, the Wittelsbachs, the Aufklärung, the Reformation, or any number of inter-imperial wars. So for the best discussions on the Empire, you have to go to period books that don't discuss much outside of their bailiwick. The aforementioned book by Wilson, The Thirty Years' War: Europe's Tragedy, does a splendid job of discussing the nature of post-Augsburg Imperial institutions and their response to the Reformation, along with Imperial politics and Imperial law. But they're only one part of the narrative.
tl;dr: read Wilson's book on the Thirty Years' War
