For every book contained in an omnibus, I add an empty book (
Add Books >
Add Empty Book) as a placeholder. Set the title, make sure it has the proper series and number, then I make a note in the comments that the book is contained within Such-and-Such other book. (I also use "Placeholder" and "In Omnibus" tags, and tag the omnibus as "Omnibus").
I really like the Add Empty Book feature of Calibre. I also use it as a wishlist (tagging empty books I want with a "Wishlist" tag).
