SSD fitting in 2012 Mac Mini?

I was dead set on getting an iMac and fitting it with a Crucial SSD, but I see how difficult that is. However, reading the blurb on Crucials website for their latest 1TB SSD, the M500, I noticed that they list the Mac Mini as an option and that nearly is the iMac so I've looked into it and the process is a lot less daunting. However there apears to be two HDDs bays in the tiny box, not sure why Apple did that as it's meant to be a small box, but there we are. My question is which one do I put the SSD into, I've seen a video where the most immediate one, readily accessed through the opening on the bottom, is acceptable, but what of the other?

How does OS X treat the second HDD, is it some kind of internal Time Capsule? How does it show up in OS X, as a separate partition? What happens if the new HDD/SSD is larger than the other? Why are there two in the first place? I also didn't glean any info from the product page on the Apple website that points to there being two HDDs.

Anyway, I think the new 2012 Mac Minis are capable of taking the M500 from Crucial, although I read their speed is taken down a peg to SATA II because of the enforced 3Gbps interface, is this true?

Thanks.