It depends.
1. Should I set up a Raid Array or use the second drive for my files and the primary drive for my operating system and virtual machines?
With two drives you can only use RAID to(1) make one large drive or a(2) copy of the first drive.
(1)Most people don't need one really large logical drive made out of two hard drives.(2) Making a copy would cut your drive space in half. You have only the size of one hard drive. This only important if you don't back up your drives.
Your last choice "use the second drive for my files and the primary drive for my operating system and virtual machines" This most likely won't use up much of the first drive.
I’m kindof thinking that I would want to use RAID in order to mirror the primary drive on the secondary drive. I’m assuming then that if one of the drives failed it would be fast and easy to resume operations without losing any data or configuations. Sort of just picking up where I left off when the drive failed if you take my meaning.