Simple answer is "Yes"
Collections can be named after series and you can add books to collections plus you can just have other books in library that aren't in collections. They act like folders in many ways but are actually meta-information... tags on the book so you can actually have book in more than one collection e.g. Butcher's "Dresden files" could be in both a Detective collection and a Fantasy collection as well as a Dresden collection.
Yake a look at calibre as well... file translation/database tool that is great for making collections and adding other tags.
