First of all, the most important thing to do is back up the data on your iPod. Although Apple tries to prevent it, it is possible to transfer music from your iPod to your computer for legitimate reasons. I suggest the open-source program iLinkPod to do this job.
Follow the instructions on the website, and you should be fine.
Once the files are transferred to your hard drive, you should immediately add them to iTunes (usually the easiest way to do this is by starting iTunes and pressing Apple-'O'). Finally, ensure that all the files you actually want on your iPod are added to iTunes, and not simply sitting on the hard disk.
Once you're sure of this, you can simply proceed by resyncing your iPod, and you should have all your media on your hard drive mirrored on your iPod.
Hope this helps