If your Primary partition is C:, use that partition. W2k will add the boot.ini to the mbr of that primary partition.
I would size it to at least 2.5 gb and format it NTFS. This will allow you to have mult.users and set various permissions levels and save desktop settings.
I have used both FAT32 and NTFS and have gone back to NTFS.
Your programs/applications should be installed to a seperate partition (FAT32) that can be shared with Millen. or W98.
W2k will go thru its install and quite a while after the install starts, will finally ask you where you want to install it. So don't get concerned.
Also if you have an IDE cdrw, pay attention and execute the F6 option when asked about SCSI devices, even if you don't have any. Then just continue when prompted for drivers.
You will be left with a boot menu that will allow you to choose which o/s to use.
To change the boot menu parameters (default partition, pause time), just edit the boot.ini file that will be located on C: as a hidden file. Use Wordpad to edit it and make changes.