I'm not sure if you've solved your problem; if not you need to realize that all programs have certain rules. Sigil will accept html code BUT it will ONLY save the html material as an epub - you have no choice. If you want to save the work you have already done, you cannot save as a html file. If you don't like this approach, you should work on your html code, combining everything, etc. outside of the epub until you have it the way you like and save it as an html, then import that file into Sigil and save the result as 'your file name'.epub.
Often I do exactly that in creating an epub - I work on the html including chapter breaks and everything that sigil insists on, then send to sigil and finish it. I think that once you get used to Sigil, you will appreciate it.