This is not something I've tried to do (and I doubt many others have either) but fit the card and let it install as usual. Hopefully, Windows will discover "New Hardware" and load the appropriate drivers, otherwise, you will have to manually load them from any disc that was provided with the card. At this point, nothing is going to change on your computer, so your no worse off.
Look in Device Manager and make sure the card has installed without any problems (no yellow exclamation marks etc).
Now connect your new drive to the controller card, noting any restrictions regarding which port should be used first and see if the drive is recognised in Windows. Assuming it is, all you now have to do is format the drive.
This is all assuming your using Windows XP, if you're using something else, please post back.