When I installed XP on the 60GB, I do NOT recall reinstalling anything that was on the 13GB drive. I just had both drives connected and installed XP on the60GB and the apps that I have on the 13GB worked just fine.
I installed office 2002 for students to get Word 2002 on 60GB. Apps on 13GB include AOL, MS-works, and Word 97. Each Word runs independently, each with a different license string. other apps are there too, so they must be looking at the 13GB drive for data.