If I understand your question correctly, it sounds like you have to tell iTunes the new location of your iTunes Music Library so is knows where your tunes are which will allow your iPod to sync to the library.
You will have to change the library location to your new drive.
The link below to the Apple web site may help you:
http://support.apple.com/kb/HT1751
Then click on the blue link titled "Copy iTunes folder to your external hard drive".
If this isn't what you were meaning - try browsing the Apple Support Web Site to see if it throws up any more suggestions.
F.