Well.. it all depends on the windows version.
When I do a fresh install of XP, I like to select the option to edit partitions after booting with the XP CD. Then select your primary partition and delete it (follow the instructions closely).
Then tell it to install XP into the unpartitioned space.. it will then repartition and format the drive automatically.
I don't think 98/ME gives you this option... and as far as Vista goes... well who knows what it's going to want to do! Win 2000 will give you this option.
If you don't like this option, and want a bit more control over things, you can download a 98/ME bootdisk from
www.bootdisk.com and boot from the floppy it will install onto. The run fdisk from DOS and you can do it all manually.