We use Lucidchart to create UML diagrams for the various flows involved, typically either like a component diagram or a sequence diagram, and embed that into a document of sorts (choose your poison: wiki, Google Doc, crumpled napkin, etc.). It's best if you follow a "test driven development" approach and design before you implement, too, though go back and update things to reflect the as-built afterwards.
In the end, though, it's about personal discipline to make it work out, so find something that you and your co-admins can actually follow through on and hold each other accountable to.
I'd love for there to be a way to document author notes on the scenario itself. We can do that using the "notes" mechanism, yes, but ideally having multimedia assets and tying them to the scenario writ large rather than a specific module in the scenario. #featurerequest
