There are many variables and preferences. I would suggest you start with an entirely new partition arrangement. Follow the link below for excellent advice.
Before you do anything, you should make a bootable floppy using the Win98 CD. Insert a virus free floppy in the drive along with the Win98 CD. Choose Browse The CD. Choose Tools, then MTSUTIL, double click on "fat32ebd". That will create a floppy with all the files you need to run Fdisk partioning tool and format, etc.
After the partitioning and formatting,(which is explained in the above link) assuming you've created two partitions, on the D: drive,type"MD Win98" then type "CD Win98". Now, type "Copy E:/Win98" and the Win98 files will be copied to the Win98 Directory on the D: partition.
When the cab files are done, simply type "setup" and Win98 will begin the install. Be sure to answer no to the Startup disk since you already have one.
I hope this helps!
[This message has been edited by Mikelh (edited 02-12-2001).]