Yep.
Matter of fact one of my benchtest machines was set up this way not too long ago...
That's the cleanest arrangement...seperate drives...you can share data etc. but the boot process doesn't see each other.Use the BIOS to determine which drive you want to boot.
Remove the Win98 drive and install Win2k on another drive jumpered as master...
When all drivers and etc. is running fine switch the Win2K drive to slave...reconnect the Win98 as master and you should be good to go.