I suspect setting up file names would best be done at the earliest point in the project.
As for everything being in one folder after Project Manager saves it, if it preserves your project structure internally, what’s the problem? If you’re backing something up because you might need to get back to it, it will load.
Preserving outs & trims is another matter. I’d put any additional assets you may need back into the same (Windows) directory in a well-named folder, just for that reason. If you’re going back to something odds are it will be to make a change downstream as much as to re-output the original.