How to manage the structure of a masters thesis and what mistakes to look out for?
Other answers have suggested outlines, but even with such an outline it's not always clear what is the best order to discuss everything (whether it's the choice of section or ordering within a section).

One approach I have seen used is to print out the whole document, cut out each paragraph, and pin them on a pinboard. Then it's easy to adjust the order of the whole document until the whole thing is coherent. You'll probably want to have a pencil on hand while doing this, because you'll need to adjust the text a bit to fit the order.