Fdisk is Microsoft's attempt at a partition manager. It will work for basic partitioning (FAT and FAT32 only, in Win98).
If you're going to install Windows 98, backup all your files first, if you can.
Go into Fdisk, answer Yes when it asks for large disk support (this enables FAT32)
Erase all partitions. If you only have one partition, you only have to remove the primary partition, but if you have more than one partition, you have to remove them in this order: all logical drives in the extended partition, the extended partition itself, then the primary partition. (It's been a while since I used Fdisk so bear with me)
Then you create a new primary partition using all of the available space. It will ask you if you want to make the partition active, you need to do this for the drive to be able to boot. (If it doesn't ask you, you should fish through the menu for the option just to be safe)
After it finishes, and returns to the menu, exit the program and restart the computer. Make sure your Windows CD is in there so you can start it up. Start the computer up with CD-ROM support, but don't go into Windows Setup yet, you need to do the format.
Once you're at the CD-ROM, type E: (or whatever drive letter MSCDEX assigns the drive, it will say it at the top of the screen) and then cd win98
format c: /s
Answer yes.
Then type smartdrv and finally setup
For Windows 2000 and XP, the process is a lot simpler. Make sure any files you can back up off the drive are backed up. Boot to the CD and start Setup. It will eventually get to a screen where you select where to install the drive. Here is where you can delete all current partitions, then create a new one. If you're going to stick with 2k or XP, you'll probably want to use NTFS, instead of FAT/FAT32.