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Originally Posted by highwaykind
That's kind of my problem with the way it is now- when I type "medical" everything that happens to have medical in the title will also show up.
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I tried to keep it simple, so I left off the "tag:" prefix for the searches I suggested. It's usually not required
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(with "medical" maybe not so much of a problem, but this tagging thing is not as "perfect" as only searching through seperate folders. (When I type "fiction" "non-fiction" will also show up).
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itimpi has the answer for your specific scenario: "tag:fiction and not tag:non-fiction"
It's true that two libraries with separate folders will keep them entirely separate, but I've got my books set up with the Calibre server. I want to be able to get all of my books from anywhere in the world. If I put my wife's romance novels in another library, I would have to run two servers.
If you read through the threads here you will find several on the tags vs. folders organizational methods. We all started with folders, and that's what we're used to. I had trouble getting used to tags, also, but I've come to the conclusion that Kovid is absolutely right.
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So I think I'll go for 2 seperate libraries (and switch through Preferences)
And then within the Libraries I will use tagging to find what I need. And then I'll wait until switching between libraries becomes a "hit the button" thing in some future update maybe 
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Why use just two libraries? Why not separate your technical computer from fiction from medical? Then why not separate scifi fiction from fantasy? At some point you realize that using multiple calibre libraries for your e-books is sort of like building multiple library buildings to house tree-books.
I'm not trying to be one of those single-minded rah-rah fanboi advocates, because I know exactly what you are going through as you get used to the philosophy of calibre's tag-oriented design. I'm just saying it's worth trying to live with tags until you are sure they don't meet your needs. Ultimately they are so much more flexible than rigid separation.
Still, if you want separate libraries, it's supported. You might also consider the command-line startup options that will let you start with different libraries.