If they are SATA drives (which I suspect they aren't if you're playing with the jumpers), make sure the drive you want as "Primary" in the first SATA port, and the drive you want as "Secondary" in the following SATA port.
Boot into the BIOS and see if you can alter which one you want to be "Primary"/"Secondary".
Have you already installed XP on the drive you want to use as storage?
If it comes down to it, just disconnect the drive you want to use as "Secondary", your PC should then only detect the drive you want as your "Primary" drive. Install XP, and then just reattach the "Secondary" drive and do what you care to with it.