Maybe it would be worth it to get a SATA instead? Mixing the SATA with the IDE as BigLu said will get messy, especially as only an upgrade rather than a reinstall job. I did not even know you could still get 20GB IDE Hard Drives.
Personally though I like the idea, as a reinstall job. Reinstall Windows on the IDE, and use the SATA as a Data Store. That way you get the security of having your Data all on a second hard drive, moving files around doesn't cause too much degredation on the Windows Hard Drive also. And if Windows fails and you need to reinstall without having time to backup, everything is fine!