Welcome to LQ. Don't worry about the hidden partition. Unless you have gone into the IBM utilities and changed the Predesktop Area setting to make it visible (the default is to keep it hidden) that space will not be recognized. To illustrate, if you had a 40G hard drive, the total available space might only show as, say, 36G.
If you are using an external USB drive, then anything you modify on it would have no effect on your laptop's internal hard drive.
Good choice on IBM BTW, I've got a T40 running Linux that is just awesome. I can't say enough good things about the T series.
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