When you install windows just have one disk connected, the one you use as your main C: drive. All data on the other disks will stay intact.
I did that with mine and my steam drive was a 2nd drive. I did have to reinstall the games but it went fast since it did not have to download all that data.
You will have to reinstall your programs, so save any and all documents, downloads and pictures if those things are on your C: drive. Yes the C drive will have its data lost, so save what you need to save.
I had read about a way to use the same drive and os, just hook it up as though it is the same board but do a windows repair.
Never tried it my self, I just do a clean install