Fellow mathematician, albeit retired. If I had to make a guess, you may not have spent enough time getting intimate with LaTeX. I don't think I've really encountered the problems you're having and, unfortunately, it has been so long since I've used it that I can't be specific.
I suspect I don't recall having those issues because I avoided them in the first place. LaTeX requires thinking about the whole document before you start it. It isn't easy to work with if you don't approach it that way. Before pressing any keys, think about the document in its entirety.
In my case, I took shorthand notes on paper, did the outline, and then began working on it. It requires a holistic view, and should be envisioned before even pressing a single key. It sounds more like you're fighting it, instead of thinking within it.
These were some of the first things taught to us in the intro to LaTeX class. I realize this is a horribly generic response, but I'd suggest you take an intro to LaTeX class to go back to learning the basics.
LaTeX is pretty versatile and I can't see any reason to replace it. It just means you'll have to learn something new, so you might just as well master the tools you already have.
Again, I realize this is a very generic reply. You're not self-taught with LaTeX, are you? If you are, then I really would like to stress the value of a good professional class. You can do an intro class in just a single semester and there's almost certainly something adequate locally.
There are probably some acceptable online courses but you may have to unlearn some stuff and I suspect a classroom will be easier for that. I strongly suspect I don't recall having those problems because I never encountere them. Of all the classes I took, the intro to LaTeX was one of the more valuable.
Heck, it has been so long that I should probably take it again. It is one of those use it or lose it things and I haven't used it for well over a decade.