well, first make sure your hard drive is set to master.
then install the controller card and hook the hard drive to it
then, simply boot off a 98 boot disk and format / partition
depending on your OS, the next steps vary.
for win2k, you boot off the cd, and begin the install. right at the beginning you MUST hit F6 and then later on it will prompt you to type "S" to add a controller and then you have to insert a floppy with the win2k controller card drivers on it...then you'll be able to tell win2k to install to that drive (else it won't see it)
for win98, you should be able to just install like normal, but after it's all installed, you will see "mass storage controller" in device manager and you must install the win98 controller card drivers at that point.
and as long as you're using an ata-100 cable (that hopefully came with the card and /or hard drive) you should be set