Its ok I have figured out why windows 2000 didnt detect Windows 98 on the other hard drive.
I ran Windows 2000 setup via booting my computer with the CD in, apprantly when Windows 98 or another OS is on a different disk you have to start the Windows 2000 setup from within that operating system. For Windows 98 it was a case of selecting Clean Install, selecting C: and then Windows 2000 detected that Windows 98 was on D: and created a dual boot system.