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Without multi-select in Sigil (which meme tells me is coming for the next release, much kudos for adding that!) splitting an omnibus in Sigil is way too painful.
What I do at the moment is open the epub in Sigil, so I can see which files belong to which sub-book. Then I create a book record for each sub-book in calibre, and copy the omnibus epub to each. If you want some "common" adjustments like to styles, do it to the omnibus before this step.
Then I use Tweak ePub for each book, deleting the files I don't want in that particular sub-book, and manually editing the .opf file in the two relevant places to remove references to them. Then just repeat this step for each sub-book.
Once multi-select is in Sigil that last step will be *much* simpler because you can do it in Sigil instead of Tweak ePub. For each copy of the omnibus you will just multi-select all but the files you want to keep in the book browser pane, a single right-click and job done, Sigil will rebuild the opf for you.
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