Welcome to LQ, IC.
You need not fdisk your second harddisk from dos. If you pop in the install CD and point it to the second harddisk (hdb?) when you get to the partitions step, you can completely overwrite whatever is there, if you want. Oh, and I advise you to install using the Expert mode, regardless of how little you think you know about either Linux or your computer... do it, it's really not that hard since there's always a little help thing at the bottom of the screen. Oh, and if you've got the bandwith, and inclination, Mandrake 9.0 is out now (I'm downloading it at the moment). Many people rave about it... I have not yet tried it, but if Mandy 8.2 is anything to go by, 9.0 should be damn good.