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As Agama said, the best way to learn how to use Calibre is to download it and give it a try. Import some of your books then pretend your old directory structure doesn't exist. Use Calibre exclusively for a week or two. And NEVER peek into Calibre's directory structure. Only access your books through Calibre's interface. If after that time you're a believer, import the rest of your books and delete the originals if you don't want to maintain two copies. If you don't like Calibre after a couple of weeks, no harm done. Uninstall it, delete your imported library, and go back to the way you were doing it before.
Now for some more specific advice. These are just suggestions and you may not need or want to use them all, but I've found them all useful in my own library.
1. You can sort in Calibre by any column just by clicking on the column header. You can sort by multiple columns by clicking on the headers in order from most specific to most general (I know this is counterintuitive, but once you get used to it, it's no big deal). Learn to use this feature to look up books. Learn to love it.
2. Create a custom column, called Subseries. Set it up as a Series-like column (with name and number).
Using Riftwar as an example, fill in your series and subseries as so:
Magician: Series=Riftwar [1], Subseries=Riftwar Cycle [1]
Silverthorn: Series=Riftwar [2], Subseries=Riftwar Cycle [2]
A Darkness at Sethanon: Series=Riftwar [3], Subseries=Riftwar Cycle [3]
Daughter of the Empire: Series=Riftwar [4], Subseries=Empire Trilogy [1]
Servant of the Empire: Series=Riftwar [5], Subseries=Empire Trilogy [2]
Mistress of the Empire: Series=Riftwar [6], Subseries=Empire Trilogy [3]
And so on. This even works for series where the suggested reading order has you jumping back and forth between several subseries, like Pern or Witch World.
3. Set up an Author Lookup field. Use the Author field to store the actual author(s) of the books, and use the Author Lookup to store the primary author of the series, or some other identifier if there isn't a primary author.
So for example any book in the Riftwar series would have "Feist, Raymond E." in Author Lookup no matter who wrote it, and any book in the Wheel of Time series would have "Jordan, Robert" in Author Lookup, even the later books that were written by Brandon Sanderson. You could put "Warcraft" in the Author Lookup for any Warcraft books.
The benefit of this is that you can sort in the following order: Author Lookup, then Series, then Title. That will put all the Riftwar books together and all the Warcraft books together. Other books by Raymond E. Feist not in the Riftwar series would appear just before the Riftwar books, in alphabetical order by title.
4. Download the View Manager plugin. Use this to set up a default sort by Author->Series->Title, and any other arrangements you might find useful. Then, getting back to the default view after playing around with sorting is just two easy clicks.
5. Set up a Save-to-Disk template that will allow you to re-create your previous directory structure. This will help with the transition, because you'll know that even if you later decide you don't want to use Calibre to manage your library, you can always export the whole thing out to the way it used to be. You may need to add other custom fields in order to store the necessary information to make this possible.
6. (I haven't tried this one myself, but your mention of chronological/reading order made me think of it) Create an Alternate Order series-like column. Use it to store the alternate order for series where there are two schools of thought on the best order to read them, like Narnia, Darkover, or Pern.
I hope this helps!
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