The major TeX format habit I've picked up isn't about file splitting, it's about inside a file: I put a newline between sentences.
If you're revision-controlling, it makes it ...actually work..., and if you're not (which, despite my best intentions, is almost always the case) it makes it much more navigable than conventional paragraph layout.

As far as file layout, I lately have sections developed in separate labeled plaintext files starting from the sketchy notes/outline/code snippets/etc. I took about whatever I'm writing about with a minimum of formatting, then integrate those parts into a single file when it's time to start finalizing. It's sort of a compromise position between a complex project with multiple inputs and spread out formatting that might interact in annoying to debug ways, and a giant single file. It doesn't necessarily make sense in the abstract, but it's been working for me.