FOULED UP PRIMARY DISK ON MY 2-DRIVE SYS

I have recently fouled up the primary disk of my 2-drive system and have purchased a brand new hard drive to replace the fouled up disk. The drive has been formatted & am attempting to reinstall Win98 Second Edition Full Version. However, th Win98 software is ditetected Windows already on my system(must be on the second drive) and is giving me and error message saying the installation cannot be done because Windows is already ont the System.
How can I completly eradicate whatever remains of Win98 on the second drive so that I can make a clean installation on the first drive?
P.S. I do not want to destroy valuable data that is on the second drive. I want to access it after re-installing Win98 SE on the new (first drive).