Hard Drive Not Recognized by OS, and SSD not a boot option but is???

I have a SSD (Kingston HyperX 120 GB) which I've loaded my OS on, amd during installation I've left my hard drive (WD Blue 500 GB) unplugged. Prior to loading the OS I checked the BIOS and the hard drive was recognized, but now when I plug it back in it is not.

What do I do?
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  1. Okay now I've gotten the hard drive recognized by unplugging both, then only plugging in the hdd (using the same wires as before), but now the SSD isn't recognized and I can't boot.

    Actually I can boot, the BIOS doesn't list the SSD as a boot option (only the hard drive and optical drive) yet it will still boot off the SSD. The OS does not recognize the hard drive though.
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