Good Read for an Intro to the general DOM thing: DOM Scripting - the code stuff will be a little basic for an experienced programmer but it's worth reading IMO
Best practices worth taking very seriously:
The Separation of Content/Structure, Presentation, and Behavior. Keep your HTML, CSS, and JS separated as much as possible via hooks rather than dumping inline JS into script tags, CSS in style tags and style attributes, and event handlers inline in the HTML. It makes it so much easier to think about and work with.
Semantic HTML - basically use HTML to describe content as much as possible. Avoid pointless wrappers and tags used simply to push layout. Don't kill yourself for this but keeping the HTML minimal and appropriate makes it easier to read and debug. The boon to accessibility and SEO are just nice side-effects compared to ease of development.
JS itself is very different from most popular languages. It's success and ability to adapt to a wide array of platforms is in large part due to that. If you know something with c-based syntax don't expect it to behave the same. Using first-class functions, closures and learning to adapt to a highly mutable language are critical skills but fortunately it's easy enough to tinker and make things happen that you can pick up basic use of it fairly quickly. jQuery can be very helpful with all the DOM stuff, but don't let it get in the way of understanding how it's done with vanilla JS and the DOM API which is all jQuery uses under the hood.
But if you're looking for "there's only one way to do it right" you'll never find it on the client-side. The problems are too diverse and too complex. You can never stop learning either. The day you do, is the beginning of the week that your skills suddenly became obsolete.
I think there's more value in O'Reilly's definitive guide than the Good Parts personally. I'm sure at least 3 people recommended that by now though. It's not a bad read. It just gets mentioned in any remotely similar question and Crockford's take on JS isn't one I 100% agree with.