Yes you can. At my school where we teach 2000, we actually have a triple boot going with Win 98, 2000 Pro and 2000 Server all on separate partitions it works fine. I would use fdisk, create the 2G FAT (or FAT32) partition and leave the rest unpartitioned, then install Windows 98 and finally 2000. 2000 will create a boot menu using boot.ini which will allow you to switch between the two operating systems.
If you make the 2000 partition a NTFS partition and ever want to get rid of it, you will have to boot from the 2000 CD, start a new installation and then delete the partition when you get to the screen that ask which partition you want to use. To get rid of the boot menu, you then have to boot from a 98 system floppy and SYS the hard drive.