I have installed win98 first edition & 2nd. via a win98 startup disk,but on a clean hard drive.
no previous operating system(s).
I'm certain fdisk/format /u commands will do via the dos prompt.
once that is done boot back up to the win 98 startup disk allow cd rom support change over to the drive letter of your cd,then type in setup.
should take.
also you will need your OEM cd key code usually on the book that comes w/the win98se cd.
hope this helps.