Perhaps something that has been overlooked in all the talk of complexity is that it is possible to start very simple with Tinderbox. If I can express it this way, Tinderbox is like a suit of clothes that will expand and grow with you as you grow.
I have done a fair bit of qualitative data analysis (for a PhD in social psychology) and also spent around eight years researching and writing a history book (long before Tinderbox existed). Something that I learned from those experiences is that it is not necessary (indeed it can be deleterious) to put in much structure at the beginning. It is far better, in my experience, to just start collecting material and allow the material to suggest what one should do with it. I have droned on about this idea before, so I will suggest having a look at the graphic in an earlier post (What is the semantic tree of personal knowledge management? - #5 by MartinBoycott-Brown) which shows research as a “system” – an iterative process that constantly loops back to the beginning and steadily refines ideas.
It is far better to start simply with a tool that is capable of handling complexities as they are discovered than to start with a tool that is too rigid to adapt to emerging understandings and knowledge.
Jotting down some notes in Tinderbox requires almost no learning of the program at all. It’s the “back of the envelope” stage – all that is needed at the beginning, I believe. Complexity can come later when it is needed.