The way I read your post, you installed each system individually to each drive, with the opposing drive disconnected. Is that correct?
The correct procedure should have been;
Install Windows 98se on the appropriate drive, and then install XP using the installer program to determine where XP will reside.
XP will then recognize the other operating system and create a boot menu in order for you to choose which system to boot into.
If my assumptions are correct, you may be able to re-create the boot file (which already exists in XP), to point to Windows 98se.
You need to find the contents of your "boot.ini" file, which will almost certainly be located on your "C" drive in the root. It is a hidden file, so you will need to go to the folder options and select "Show hidden files". Once found, open it with Wordpad or something similar, and post the contents here, and one of us will try and work out what should be there.