@delta888 - welcome to MobileRead.
Sounds like you are talking about "Omnibus" editions, a search for that should reveal some posts to you. To answer your question people do it in different ways. Personally I often end up splitting the omnibus into the individual ebooks using Tweak ePub/Sigil so it isn't an issue
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However other approaches I have seen mentioned/used is to add information to the book title in brackets like "Foo (Omnibus 1-2)". or add a tag to say "Omnibus". Or give it a series number like "99" or "0".