This is a large subject, but it isn’t well served by a large essay, so let me be as brief as I can. I do a huge amount of thinking about things; probably an excessive amount. I think about work, and facts, and ideas, and theories, and projects. I think about what I need to do, and what I ought to do. Perhaps you do too.
Keeping track of our thoughts in that regard can be tricky, but there’s a single principle which will absolutely make it easier: that of atomicity. A thought has to be graspable in one brief session, otherwise it might as well not be there at all. The way to achieve this is to ensure that there’s nothing else you can possibly take away from it: make it irreducible.
If you’re writing an outline for a book, for example, break a bullet-point into further sub-points so that each one is atomic. If you’re writing software, decompose the functionality until you have atomic units of execution. If you’re putting together a plan for redecorating the bedroom, make a task list and put every step onto it.
There are many informational structures which help with different aspects of the process, and the most important of them is probably the wiki. Wikis have some advantageous features like backlinks (lists of pages which themselves link to the current page) and connection graphs, but those things are conveniences rather than the true killer feature. The killer feature is that wikis make it trivially easy to break information into chunks, by creating a new page at any time, and they then allow you (equally trivially) to refer to that information from anywhere. It is the inherent focus on decomposition and atomicity which makes a wiki — or any broadly similar structure, in terms of unrepeated and irreducible units of thought — so incredibly powerful.
You don’t need to actually be using a wiki. Perhaps you’re creating lists and sub-lists in a to-do app, or maybe you’re making judicious use of the one-scene-per-sheet approach in a writing app, or something else. The essential factor is that you’re breaking it up, and then connecting it back together. This seems to be how our own minds work, and it’s certainly the approach that I find most conducive to well-ordered and insightful thought.
Don’t plan or summarise in prose. Don’t write in monolithic manuscripts. Don’t code in complex routines. Not only are these approaches unmaintainable, requiring a burdensome amount of contextual information and recall in order to even be usable, but they degrade your quality of thought. The wider the angle, the fuzzier the details, because there are more of them. Get closer, though, and the fine detail becomes clear.
There’s a physical sensation like the unclenching of a fist which comes from atomic thought. Relational thinking brings perspective, true context, and high-quality insight. It’s a lesson which first-year programmers are taught, and it applies to virtually everything else too.
If you can’t hold an entire idea in your mind, crystal clear and ready for manipulation and expansion, then you haven’t broken it down far enough yet.