Take a look at "plugboards" in Calibre. This is a feature which allows you to automatically prefix the title of the book with a series name and number.
Eg, if Harry Potter eBooks were legally available, which of course they aren't, you could have:
Harry Potter 1 - Harry Potter and the Philosopher's Stone
or whatever.
The series name and number will be automatically written to the book when you transfer it to your reader.
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