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Capricorn - my, rank layman's understanding is that there is no right and wrong.
Calibre editor shows the files according to type under labels such as 'Text', 'Image' etc but they're not stored within the ePUB in separate directories (folders). Whereas Sigil does store different types of files in different folders.
Best way to get to greps with what's going on is to save two copies of the same ePUB from Sigil and Calibre, and then look inside them with an archiver like WinRAR or 7zip.
What matters is that the files are named and located as they appear in the manifest.
Is one better than the other? Dunno - try the Religion and Politics forum
BR