Well, the fanon categorization and template guides in our policy section give a full outline of it. Basically, the property template goes at the top (property other in character and event pages, etc.) The author template goes at the bottom - that jut has your name and a link to your fanon category. Everything has "A to Z (fanon)" and some subcategory of your story on it, like "FANONNAME chapters (fanon)" or "FANONNAME characters (fanon)." Actually, if you go to this page and create the page in the appropriate field, all the templates and categories will be there for you. You just have to fill in the appropriate information :)
They're only disabled on Legend of Korra articles until a month after the finale (July 23rd). There was a flood of spam comments on those pages, so some users made a forum about it. I definitely support comments, but the compromise came up with made them centralized to a blog on those pages until the 23rd.
Oh, it's been pretty heated from the beginning. It started in this forum, then it sparked a sequel and a triquel. Plus there have been numerous blogs written about it, one of which was written by someone who I don't think visited the wiki until now.