I'll either number it 0, or the first place appropriate in the series (e.g. 4.5) and then add empty books (use the drop-down arrow next to Add Book) for the remaining stories/novels in the omnibus. I then give them the appropriate titles and number them properly in the series. Then I tag them "In Omnibus" and "Placeholder", and put "Contained in ___" in the description.
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