The most productive way for me today is once I have a complete story form I copy the "Story Engine Settings" Report into a Word document. The documents becomes later my binder for all my illustrations and research material for the current project. I usually have one word document full of stuff (filled-out storyform, notes for theme and character, misc) when I start my first draft.
When I copy the contents of the report first time into the word doc, I make a table with two colums. Whats before the double dots (MC RESOLVE: Change) in the report comes in the first column, whats behind in the second one.
If I change the story form later, usually that happens many times, I override in the word doc the second column manually with the new selections - but can keep my illustrations.
I have tried to work directly in dramatica but this is to cumbersome epically when it comes to copy and paste notes from one section to another one.
I also tried Excel, but Excel doesn't really work for me as it is to "technical" and hinders my muse to work.