I don't understand the question.
If you boot with a "boot floppy", you will get an A:\> prompt from which you can run the FDISK and FORMAT commands from the floppy. (A Windows 98 floppy is more 'complete' than a Windows ME one.)
However, you seem to have got past that stage. If you boot with the floppy using the option to have CD-ROM support, you should be able to change the prompt from A:\> to that of the CD drive (temporarily displaced by one letter, so D normally will now be E). Then run Setup.exe from the E:\> prompt.