Looks like @scrive just above has given some well experienced advice - well done.
Here’s a page which might give something further on the entering equations part - several items in it:
[url]How to input latex math equation in scrivener?]
I suspect several would be interested if you continue this thread with some report of how it goes, and what you find you want to use.
Also if it continues to be Latex, though that sounds an ideal way to get Scrivener’s benefits for the whole thesis construction while keeping the maths embedded…
Best fortune on your endeavors!