This thread might help you. The way that you want to organize your collections sounds similar to how I have created mine using the powerful features of calibre.
https://www.mobileread.com/forums/sho...d.php?t=160853
I have mine sorted first by categories (generes) and then by series. There is a photo in this post.
https://www.mobileread.com/forums/sho...0&postcount=82
I explained the learning process of how to use calibre in this post:
https://www.mobileread.com/forums/sho...0&postcount=96
Hope that helps!