What are some good ways to structure material before writing a theoretical paper/thesis/book?
Of course, it's disastrous to be so disorganized that things get lost, work has to be duplicated (even if it's just typing), etc.

On the other hand, I observe that many novice writers over-allocate their time+energy to "planning". I say "over-allocate" exactly because (as in the question) when one doesn't have too many details about the sequel, it is hard to plan. Further, especially in thesis situations, and, even for more experienced people, in book writing, the very process significantly changes one's viewpoint, so that an initial plan/outline/table-of-contents/statement-of-intent easily becomes grossly inaccurate over time+experience.

For example, although it is interesting, and an interesting exercise, to try to write an introduction or preface at the beginning, it will most likely prove wildly irrelevant, and have to be scrapped nearly entirely. 

A second crucial mechanism is (as suggested in the questioner's self-answer) feedback, and, equally, iteration of the writing/editing cycle. 

The two concepts combine to suggest that one should not waste time doing nothing, but pretending to be trying to fathom what one will think, and what one will discover, some months in the future. Hesitation delays the very experience that will bring to life one's future viewpoint! :)