I flashed the bios and now the ssd/hdd are both showing up. When I set the SSD as the first boot option and the UEFI: Windows Boot Manager to the second option, I got the "Reboot and select proper boot device" error so I had to unplug the SSD and HDD to get into the bios and change around the boot options. I plugged the SSD and the HDD back in and when I got into the bios I changed the UEFI: Windows Boot Manager to the first boot option and the SSD to the second boot option and then Windows booted up fine. I think that I may have messed up the installation of W. 8.1 on the SSD because both the SSD and the working boot option are showing up on the boot list.
It's an MSI Z77A-G41 mobo. SSD is an 840 Evo 250gb and the HDD is some WD green 1.5tb drive. I installed Windows 8.1 with just the SSD connected but I think that when I was creating a bootable USB I used a zipped .iso file which may have contributed to the problem (?).
The SSD is connected to the Sata1 (lowest) port and the HDD is connected to the Sata5 port.