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Danger is correct. The epub is a bunch of files in a specially made zip format. If you open one with winzip, you will see what we mean. That is also the place Sigil will save the toc.ncx, because according to the specification it must be there.
When you insert a xhtml file into Sigil you can do what you want with it. I personally split every chapter into a separate file, after some standard post-processing from my side. That makes it easier for me to work with and maintain.
You can do either way, the resulting epub will work. You will just have more files in the epub-file. However, please keep in mind some things.
1. Some readers have a 300kb limit. That means that one XHTML file must not be larger than 300kb.
2. A small file reads faster in a reader than a large file.
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