You have master boot record files on the HDD - you'll need to backup the data, wipe that HDD and copy your files back over manually. For the moment, disconnect that drive until you can complete the data wipe.
Now, install windows with just the SSD connected to your motherboard. Allow it to format the hard drive (delete both the partitions within the selection window when it asks where to install the OS).
That's about it - make sure that you have AHCI enabled on your motherboard's BIOS or it won't pass TRIM commands and you won't get the speed you're hoping for from that drive.