Whenever I build systems, I usually make the first partition 15GB for the OS boot. Too many people overshoot the usage of the boot drive, and end up assign like over 25GB. Unless you go warezing like insane, you generally don't need more than 15GB for a solid boot drive.
BTW Mattlock, you sure about that second HDD, a 13GB Maxtor ATA100 7200RPM? In one of my old systems, I have a 13.6GB Maxtor, ATA66 7200RPM. If it wasn't for the increased aureal density on the new D740X HDDs, I would actually recommend you to install the OS on that 13GB HDD. Reason being, you can simply swap that drive in and out. If you put your boot partition on the 40GB HDD, and have another partition it becomes a little less organized. You're using storage partitions on both drives, and one shares space with the boot drive.