You can do it two ways (or more). First, you can simply put all your music where you want it, then throw away the iTunes Music Library.xml file that sits in your iTunes folder under user/Music (don't do this if you have songs rated or other customizations, as they will be lost). Then, simply go to the File menu in iTunes and select Add To Library and add your folder or folders once for each hard drive (it helps to have all your music in one folder per hard drive for this step, even if it is broken down into multiple folders within that folder--ie, duplicate the directory tree that is default for your iTunes Music folder on the internal for the external or make it easy to find and remember on the external). The disadvantage here is that I believe you will not be able to burn CDs of songs that you bought off iTunes Music Store unless they are on the internal CD (at least that's what I found on my computer).
Second, you could download and run this:
http://www.versiontracker.com/dyn/moreinfo/macosx/13554
Good luck.
EDIT: Mitthawnuruodo's message was not there when I was typing mine, therefore the duplicate recommendation of iTunes Library Manager.
