The Win98 boot floppy usually creates a temporary ram drive that moves your cd drive down a letter until Windows is installed. So if was D it will become E.
I'm trying to remember Win95. I think you choose to restart and select command prompt only. This should leave you at C:>. Just type format c: to format the drive.
When formatted switch off and put the floppy in the drive and switch on. A number of Files will load and you will be left at the A:> prompt. Type E:setup and Windows should install.
You will need to make sure that you have all necessary drivers (video, sound etc) for 98 as well.