On first installation, MC will do a search and try to find your music. It does a count down timer in the lower left corner telling you that it's going to go find your files and install them. You can stop this by clicking the button on the timer. Sounds like it found a bunch of your files and imported them.
I would start by clearing your library entirely. That will remove all the imported media from the database, but will leave it all on disk where ever it is. To clear everything out of your library:
File > > Library > Clear Library
Now you need to import some files. You can do that directory by directory if you'd like:
Tools > Import > Import a single folder
This will import everything in the folder and everything underneath it. So you could import your "Music" directory and it will also import all files and folders inside of Music.
You can also set up MC to do monitoring on one or more folders. So that any time you add new files to a folder (or subfolder), it will find them and import them. This is called Auto Import:
Tools > Options > Library & Folders > configure auto import
I like auto import, but it might not suit your needs.
Good luck.
Brian.