I'm in the process of purging out the bad documentation.
The only reason why I haven't done it completely is because I need to implement the new-style navigation here -
http://www.stencyl.com/help/ - first, otherwise there'd be no articles to look at. I'm actually working on that part as we speak.
The crucial chapter on building/designing logic is in the works right now by Joe, who I think will have something ready by the end of the weekend.