Here's the best way to do it:
Partition your new drive into C: for 98 and D: for 2000. Then boot into 98 on your old drive. Go to the run command and type:
xcopy32.exe c:\*.* e:\ /c/e/f/h/r/s
Where C: is the current 98 drive, and E: is the new to-be 98 drive. That will copy all the files off your 98 drive, including all hidden, protected, and system files. Then, do the same thing to copy your 2000 drive to the new one:
xcopy32.exe d:\*.* f:\ /c/e/f/h/r/s
Where D: is the current 2000 drive, and F: is the new to-be 2000 drive. Make sure you're still in 98 when you do that, cuz 2000 doesn't have xcopy32.
After that, hook up the new drive as the primary, and boot from a 98 boot disk, run fdisk, and set the C: drive as an active partition. After that you should have your system back to the way it was.
Rob