You can import two pdfs, epubs or whatever with the same title. When you import (both at the same time) it imports them, and then asks if you want to keep them both even if it's the same title.
I had the problem with a pdf which consisting of 12 pdfs, all with the same title as it was chapters in the book. Calibre imported them, then asked if I wanted to import them even if they have the same title. I clicked yes, and they're all there now.
After that, I "catalogued" them, and also swapped title for "author" (as the author metadata had the chapter numbers).
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