You can install Windows NT4/2K/XP on an NTFS partition without it affecting Linux. You just won't be able to write to the Windows partition from Linux. Linux supports read-only for NTFS partitions, and read/write for FAT partitions. Only install it on FAT if you want to mount the partition from within Linux.
The easiest thing to do is install Win2K first, and then Linux second. When its time to install GRUB (or LILO), tell it to install into the MBR. This will overwite 2K's boot menu and you will give you a GRUB boot menu when you start the computer. You will be able to choose between Linux or Win2K. If you don't overwrite the MBR, then you will need a floppy to boot Linux, which, I would assume, you don't want?
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