The confusion you write of is very common and even shown by how books are formatted coming out of the various Project Gutenbergs.
Instead of using headings to indicate this is the top of the document, this the first level below that, etc., they use headings for formatting. This makes for a lot of work in Sigil when you are trying to use Tools, Generate Table of Contents. You end up unchecking line after line because they are not Contents or Chapter I, or subheadings under those, but information about the book, or lists of other books by the author.
Many of the PG books come out looking very nice, but the tools like Sigil are based not on appearance, but on using headings, etc to indicate how the book is put together, so it is not surprising the OP is having trouble.
Everyone has their own aims in doing ebooks. I do not make them for other people, so I can indulge my own preferences and I don't want to work too hard at doing it. I have my own customers in my repair business I have to keep happy. I do not have to worry about that in my epub creation.
I have been pounding away at it for 5 years now, so HTML and CSS have begun to make sense. (I had a little edge because I made my own simple web pages many moons ago.) But it is possible that if I were just starting now I would just use Atlantis or Jutoh, so long as I could get the results I want. I am making a book of local flora and fauna appropriated from various web sites for just my own use and am using AWP because it is easier to cut and paste into it. For things that are already HTML or convert to HTML, like the US Army's book, Merrill's Marauders, I use Sigl.
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