the key here is "seeing each other"
I have an idea (just pulling this off the top of my head here)
Install Win98 on one partition (formatted fat32) - make this the partition for your son to game on
Install Win 2000/XP on the other partition (formatted NTFS) - make this partition for you
Since Win98 can't read NTFS partitions, your stuff won't get infected (Unless the virus infects the boot record, or CMOS)