Hello Francine
The bad news is that Windows ME MUST reside as the c:\ drive. So i recommend that you make the smaller disk the "master" in this case. Check out the jumper settings on both disks so that the smaller is the master and the bigger is the slave, or set up the second disk as the secondary master with your DVD/CD-ROM drives as slaves.
To partition the hard drives you must either drop into DOS and run "fdisk" from the command prompt, or boot from you Win98 boot floppy and do the same.
First, partition the smaller (master) drive using fdisk. Ignore the larger drive on which you will install Windows 2000. The idea is that there will be no conflict with assigned "D" drives (i.e. CD-ROM)Also, fdisk will format the second drive as FAT32 when it would be better to set it up with Win2000 under the NTFS file system. Set it so that you create a maximum partition. Format the drive from the command prompt (your WinME manual should tell you how to do this)Don't worry about the bigger drive at this point. When you install WinME it will ask you about configuring unused space. Ignore this.
Once WinME is set up on the disk, insert your Win2000 CD. Create the necessary partition (just follow the instructions)and format as NTFS. Now,when setup is infull swing the program will recognise that you are performing an upgrade and you should be asked to confirm the identity of your qualifying CD (i.e. Win98 by inserting it into the CD-ROM for setup to confirm). In other words you shouldn't have to install Win98 first to upgrade. This is important as Win98 will more than likely overwrite your WinME boot info on install as the two OS's share the same system attributes and are thus not compatible for dual boot without third party software (i.e. System Commander, Boot Magic).
I have to admit that i am "assuming" that Win2000 upgrades follow a similar path to Win98/ME upgrades. My own install was a full one.
Windows 2000 should boot into "E:\" drive status. As you have used the NTFS format you will not be able to detect Win2000 from the WinME install. However, if you want you can format Win2000 as Fat32 on setup (the same as Win98/ME)inwhich case the two disks can read and write to each other but only in a very limited way.
So, format the smaller disk as FAT32 with WinME, and leave Win2000 setup to format drive (E:\) as NTFS (you get all the great security/encryption facilities this way).
If you need any more help don't hesitate to email me. Otherwise i'm sure that another forum user will correct me on my assumption about the Win2000 upgrade path in the meantime!
Good luck!