How can I best configure this hard drive?
You can partition the 2nd drive leaving ample room for the system software. Then you can install the system onto the 2nd drive or clone drive 1 onto drive 2 and have a backup of everything on drive one. Cloning allows you to use the 2nd drive as a startup drive. The downside to cloning is that you copy the entire contents from drive 1 to drive 2.  Installing the system software avoids this problem. But as @Steve Chambers said, if you just install the system and hard drive 1 fails, you need some way to get the data off drive 1. If you clone you have the data from disk 1. But it will become dated the longer you use disk 1. I'd suggest you install just the system on Disk 2 and you should be able to use the other partition for whatever you need.