Ducks, your sorting is a lot like mines.
@Davi,
Basically, you can set up Calibre to create the folders to sort your ebooks for you. So for example:
{series}/{series_index}-{title}_{author}/{title}
looks like this...
Twilight/2-Full_Moon_Stephanie_Meyer/Full_Moon.epub
So then the Full Moon ebook is in the folder "2-Full_Moon_Stephanie_Meyer" which is in folder "Twilight". Since Full Moon is the second book in the series, there's a "2" in the subfolder.