Look in the root of the drives for a file called "Bootsect.dos". The root of the drives is when you open the drive but do not enter any folders. It may be under C:\bootsect.dos or E:\Bootsect.dos
If you had a bootable version of DOS when you installed either windows 2000 or XP, that file would have been created and thats what the 200/XP boot loader uses to boot DOS or windows 95/98
You can't add DOS based versions of windows to the boot.ini file directly like with 200 or XP. The boot.ini file needs to load a bootsec.dos file that in turn starts DOS.
What is the 16MB FAT partition?
As for the CD Rom drive, I'm assuming you must have other programs in DOS because I don't know what good a CD-Rom will do for partition magic.
But I think the most common driver is Oakcdrom.sys If you have or can get a hold of a windows 98 boot disk try that driver.
You will need to add it into the config.sys file just like the other driver is listed.
Autoexec.bat and config,sys are hidden system files, you need to change your view settings to show all files and to unhide system files in order to see it.
How often do you need to boot to DOS?
If you really want to add it to the XP boot menu I outlined about 4 different ways to do in in this topic here:
That person was using XP embedded and because it didn't have a lot of the standard files and runtimes of "real" XP it took several options before one would work on his system.
But each and every one worked on my regular XP system.
I think the easiest may have been the last one I suggested on the second to last page using debug.exe (also from a windows 98 boot disk and you may already have that in DOS 6.22
You don't need to use a boot disk since you have DOS installed and bootable, you just need to put the files in the DOS partition and boot it.
If you decide to go that route, ask any questions you want first and I would not suggest making any changes unless you have your system backed up or you have a way to recover the XP boot if necessary.
All my examples in that topic are using one hard drive with XP and DOS partitions. It's going to be a little different using 2 hard drives like you have.
Dave