As Dave says you could format it by using a 98 boot disk.
Unfortunately it depends how you have set it up initially Michelle.
If you have done a dual boot setup in the usual way then when you installed XP it will have altered the master boot record (MBR) which will be on your 98 OS drive.
If you try and fomat that drive from inside XP I dont think it will let you do it.
As Simon says it will know that its a system drive.
If you have installed XP on the drive while the 98 OS drive was disconnected then each OS/drive will have its own MBR.
In that case you could format the 98 OS drive, but it would give a warning that I think you could override.
Or you could do it Daves way.
When you start the pc does it take you to a screen that asks which OS you want to boot from and that you select by using the Up and Down arrow keys then press enter ?
If so then you have set it as a standard dual boot and I think that even if you disconnected the 98 OS drive as the XP drive would no longer have a MBR then it wouldnt boot
The same would happen if you formatted it by using a boot floppy.
Has he a lot of stuff that needs saving on either drive as the best way would be to save everything he needs to one drive then disconnect that drive by pulling the power lead or the ribbon cable from that drive.
Set the other drive as a single master by using the jumper and then reinstall XP on that.
Dont forget to do as I told you before and to delete each partition then create a partition of the size that you want to install XP on.
Then you can connect the other drive as a slave, transfer the data to the XP OS drive, if you have enough space and then format the slave drive and transfer the saved data back to the slave drive