I would make two partitions on the OS drive, one for root (mountpoint = / ) and one for home (mountpoint is /home ). You can just make a root partition, but if I ever go to another OS I can leave the /home partition the same and carry all my configuration and settings over.
Then you should format both blank ide drives and create mountpoints for them. The mountpoint can be anything. Like /hd1 and /hd2 or /firsthd and /secondhd, it doesn't matter. But make sure to know the actual location of the drives and partitions. An 'fdisk -l' should tell you that. Like if the first ide hard drive was on the primary controller and was the master device, it'd probably be /dev/hda. And the first partition on that drive will be /dev/hda1, the second partition will be /dev/hda2, etc. So if you wanted to mount the first partition on the hard drive on the primary master controller you need to mount /dev/hda1 to the mountpoint /hd1 and if you change the directory to /hd1 it'll go to that partition.