wh booting from the bootdisk you will get a question how you want to boot: with or without CD-rom support. Choose "with"...don't take out the bootdisk afterwards.,,it could cause problems....you can take it just before Windows98 starts to install, it will ask you to create a bootdisk, select "no" and take out the bootdisk.
When setup is almost finished it will reboot and automatically proceed to finish the installation. You don't need to use the bootdisk anymore.
Maybe u have to change the Bootsequence back to c: first in your BIOS. It depends on ur BIOS. If it asks for a floppydisk after installation u need to change this in your BIOS.