gtvr is quite correct - see this M$ article:
http://support.microsoft.com/kb/307881
So if you do this you will have Win 98SE on one HDD installed first. That drive will be formatted with a FAT32 file system when Win 98SE is installed, and that OS will be able to access that drive.
When you later install Win XP on the other drive, it will be Formatted as an NTFS volume, and you will be able to create a dual-boot option so you can select which OS at each boot time. Win XP WILL be able to access BOTH drives because it has support for both File Systems. However, Win 98SE will NOT be able to access data on the other drive because it does NOT know NTFS.