I have a similar set-up here ATM, two HD's in the one machine. Both have Win98 installed - second one used mainly for backup and/or trying out game demos and other software without fear of doing any harm to HD that is normally used.
To use the second HD and the copy of Windows on it I simply alter the BIOS so that it tries to boot from the slave drive first. That way there is no need to open up the case and change any jumpers or swap cables around. HTH.