Yes, it will be automatic...which is what I am a little worried about.
I imagine I am going to get a bunch of bug issues of "why is X not working like it used to", "what happend to my shortcuts", "where did my colors go", "Why are my setting in BracketHighlighter.sublime-settings not working". I am going to have probably a good couple weeks of a lot of people freaking out without reading the documentation. I wish I could get the messages.json working properly with my package in Package Control, but I never have figured it out.
So really if you are waiting for the official version, just sit tight and you will automatically get it. I wanted to get it nice and stable and ensure that my new design was not going to have negative effects before I pushed it out on people...but if your curious, it is working real nice .
I realize the new settings file(s) are a bit more complicated, but this allows custom brackets which people seemed so badly to want. The more flexibility that is desired, the more complicated the system. It saves me a great deal of trouble though, because now custom brackets can be added without me ever touching the core code...I can't tell you how happy I am about that .