MC does not move (or copy) any of your files from disk to disk (or anywhere) when you Import the files, like iTunes does. This is just the process of telling MC that they exist. So, you will generally just want to use MC's Auto-Import setup to watch the appropriate folders on your external disk. The wiki articles Arindelle linked to above are great places to learn about this (I wrote or edited most of them).
One thing, to be clear, MC uses the concept of a
Library. In MC's parlance, this just means "database", and is
distinct from the media files that make up your personal "media library" (big L versus small l is the way I like to describe it). When you import files, you're adding them to your Library (but as I said above, this does not move the files around at all, just adds records to MC's database).
The reason I bring all this up is that the
Library itself should not be stored on your external disk, as that will likely cause performance issues. For more information on this:
http://wiki.jriver.com/index.php/Troubleshooting_Network_and_Slow_Storage#Library_Location_on_DiskMC's Library is quite small (it is just a database) and storage size constraints are not a substantial concern, but it really wants to be on a fast disk (preferably the one with the fastest random access speeds, which would almost always be an internal SSD).