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My advice:
1. Think about how you want your books organized before you start adding them to Calibre.
Some possibilities are grouping them by broad genres (SF/Fantasy, Chick Lit, Historical, Mystery, Contemporary, etc.), using broad genres along with narrower hierarchical sub-genres when applicable (Mystery, Mystery.Noir, Romance.Historical, etc.), using free-form tags that help you remember details of the book (hidden magical world, chosen one, orphaned protagonist, hero's journey, England, Scotland, Quidditch, etc.).
You can use a combination of these, too, but I find that keeping genre and freeform tags in separate fields works best. I've created a custom column for freeform tags, and use the built-in Tags field for BISAC categories.
2. Look at the available plug-ins and consider what might provide utility for you. I use a ton of plug-ins, but the ones I find indispensable are: Count Pages, Extract ISBN, Manage Series, Overdrive Link, Quality Check, Reading List, View Manager, and a few that provide more sites to collect metadata from, like Barnes & Noble, Goodreads, FictionDB, Kobo Books & Webscription.
Since some plugins use custom columns, I think it's easier to get them all set up before you start adding books to the library.
3. Add, download metadata for, and fix tags on books one at a time. You don't have to do it all in one go; I clean up metadata while watching TV or listening to audiobooks, 20 or 30 books in an evening. It's less time consuming to do it right the first time than to have to go back and clean up a disorganized mess later. :-)
There are automated ways to handle metadata import, but I find doing it manually to start with is a better way to get a feel for how you want the process to work. Once you're sure that your tag scheme is working well, you can look into filtering imported tags, etc.
4. Check out the custom columns thread to see how other people are organizing their libraries; you might get some ideas.
That's all I can think of off the top of my head. Good luck!
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