Calibre is a massive program, it is easy to understand feeling overwhelmed if you look too far under the hood too quickly
Going back to another of your original questions of the Riftwar saga example. You shouldn't need any custom columns or user categories to both store that information in Calibre and output it to disk. The title, author and series columns will store all the information you need for that.
What to do next depends on where you want to export the books to - are you wanting to send them to an ereader (if so then what device), or are you wanting to save them to a folder on disk? If you give some specifics then I am sure people can suggest any changes if necessary to your save/send to device templates and plugboards.