If you got Win98 OEM (or full) version, it can only install on a "new" handdrive, i.e. reformarted and repartitioned. You need to parpare it with fdisk etc which normally on flopyy disk. If you got upgrade version, you may be able to go to win98 CD and type setup to start. on c:\ type d:, it should get to CD drive if your HDD only has one partition.
If you got original Win98CD, it should be bootable, you can get into bios setting and make CD the first boot device and boot the system from CD, and then just follow instruction. If the CD is not bootable, you need to boot from a floppy and go to cd drive, find setup.exe file and run it. If you do not have a bootable disk, you can download one from bootdisk click here.