I have pretty much everything written down in some form, as far as major or minor plot points go. Even the random funny fillers I have to put down just for recording purposes.
I do allow for extra minor arcs and changes as I write/board out the immediate episodes, like the Blind Owls was sorta thrown in at the last moment, to accommodate a holiday and play around with an idea (and bring focus to other characters for a change).
I've also decided, after a few years of drawing and one year of publishing, to reformat the series based on major arcs - The White Order, Red Order, Brown Order, and Black Order, each encompassing overall themes (White=knowledge/enlightenment, Red=violence/action, etc). And it doesn't interfere with the story, it just helps me sort out where to put certain arcs/episodes and order them accordingly.
I do try to stick very close to character development points though, cause to me that's more important than what happens to them (truth is, they don't always change from major events - like after the Pestilence, Friar's still kinda the same at this point, but they will morph/shine at certain planned points, and until they happen, I have to preserve the "before" image without diverting too much from it.) Guess it's me trying to keep some things fresh despite having stuff planned out. As long as I don't add too much detail or go off track, it'll be okay (I do have consistency errors, particularly in setting, but once I figure it out (map it out in 3d), it'll be corrected--going forward, or until I decide to do a redraw)
It's my first (published) story, so I'm open to learning on the fly.