Current drive = '98 (set as Master); you want that drive to be Slave to a new W2K Master and have a dual-boot???
Presuming so then you "will" have problems with path statements for '98 - when its drive is in Slave position... '98 was installed with its path references to c: - now it will be d: or whatever... '98 will not boot - if its current drive is Slaved... Using an add-in boot-util may allow you to overcome it but I'm not totally sure about that...
Leaving '98 as Master to the new drive (set as Slave) and installing W2K to slave posn will preserve all path statements for '98 - and allow dual-boot (with default OS to boot option as you wish). However if '98 drive is significantly slower than the new W2K (Slaved) drive then the newer (Slaved) drive will be obliged run at access/rates of the older '98 (Master) drive... This may or may not be an issue you can live with???
Presuming you do go with '98 as Master to W2K Slave then it's relatively simple to set it all up. Preconfigure/preformat the W2K drive using a '98 bootdisk (Fdisk/format utils). Then run W2K setup as per norm; point it to install to Slaved drive posn. W2K will deposit its boot/start-up files ino the '98 c: root - the actual OS (system files) will go where you point them (on W2K/Slaved drive). The dual-boot will be established automatically - and (by default) W2K will set itself as default OS to boot.
Preconfigure the (Slaved) W2K drive to have both Primary and Extended partitions; Primary for OS etc., Extended for shared data.
If you really want to have newer drive as Master then you could transfer/copy '98 to that drive - using utils provided by the new drive's manuufacturer? It would go into the Primary partition (the drive would have to be preconfigured to have at least two partitions (Primary/Extended). Ideally again you would have a (third) shared partition (a logical-drive) for data, and W2K would be in the first logical-drive. Then you install W2K as per norm.
Once dual-boot established, simply use current '98 drive for data. You could leave current '98 installation intact - although it won't be bootable, or delete it as preferrred.
Need more input/clarification - post back?