7426k:
Are you saying that you have a single partition on your external HDD, that you have moved your iTunes Music folder there, and you also backup to the same partition? If I understood that right, it is not a very efficient operation.
+Can I somehow tell the external drive to create a partition outside of which I can place ITunes and the music so that when it makes a backup the Itunes files don't get erased?+
There are several utilities which claim to be able to partition on the fly:
iPartition
Volume Works
DriveGenius
Of those three, the only one I have reports of successfully completing partitioning on the fly is DriveGenius. However, you are talking about additional expense, and if this is your only copy of iTunes, you risk losing it if anything goes wrong.
If you have not yet deleted the iTunes Music folder from the internal HDD you may be better advised to partition the external HDD with one partition approximately the size of your internal HDD, and other partitions as you wish, one of which will house your iTunes music. That is the optimal way to go about the procedure. In any case, I believe you should be looking at a larger HDD for your iBook before very long.
You have run into the classic issue with SuperDuper. It is a great utility, but it does erase the destination drive to create an exact copy of the source drive. I suggest that in this case you use
Carbon Copy Cloner. Download the latest version. Then uncheck the box to erase the destination drive. I suggest that after you download CCC that you carefully read the documentation before attempting anything. Since your only backup is at risk, you cannot be too cautious.
Please do post back should you have further questions or comments.
Good luck.
cornelius