Theres many ways a second Hard drive can be set up.
1. As additional storage - alternate to the primary HDD
2. Redundancy - If your hardrives are both Sata and you have a RAID controller, Setting up a RAID 1 (mirror) will create reduncy so that both drives contain the same data, If one dies, your other will continue on as if nothing happens. Replace the dead drive, rebuild the mirror, and your computer will enjoy continued redunancy.
3. Performance - RAID 0 (stripe) your 2 drives will act as 1, theoretically, giving you double the performance of just a single drive. Of course, now you are twice as likely to lose data because if either one dies, your SOL.
4. SSD - buy an SSD, install your games, and programs on it, turn your existing HDD into additional storage. You will enjoy a ton of everyday performance, as well as your games and programs loading MUCH FASTER! The biggest problem is that SSDs are expensive. About 100-120 for 60GB. But very worth it in my opinion.