You do not have to multi-select files to generate a table of contents. In fact one chapter per file is the norm. So as long as you use heading tags in each file (h1, h2, h3) to mark the chapter and section titles, you can use Sigil's Create Table Of Contents tool. In epub2 it will recreate the NCX, in epub3 it will recreate the NAV, and there is an option to create a HTML toc as well.
You might want to take a look at the Sigil User Guide if you are new to Sigil.
It can be found here:
https://github.com/Sigil-Ebook/Sigil....25_epub3.epub