Hi, cueshark.
Follow @shivababbli's advice, but when you boot your computer, do that with just the SSD connected to the motherboard. It should take the C drive letter automatically. After that, go ahead and connect the HDD (backup any data if you need to) and then repartition and reformat it however you like and choose the letters for the partitions yourself.
Hope that helps.
Boogieman_WD