TidusJames :
Honestly, I would add both drives to the same installation. Run the os on the SSD and games or anything else on the HDD. Ive got 8 drives in my PC. I even use a program called Steam-mover to creat junction points that basically move a folder and makes a pointer right to where you mvoed it to. So i can have steam on a 2TB but put certain games on my SSD with about a minutes transfer, then play them with the performance of a SSD.
Agreed.
It makes little sense to have two different drives with the same OS on them.
Keep the SSD as the Windows drive and migrate like this:
1) Install "Program X" on the SSD
2) Transfer (copy/import) any relevant data from Program X
3) Repeat for all programs
4) Import any other relevant data ("Documents" folder etc)
5) DELETE all Windows data on the hard drive (just delete the folder on the HDD while in the SSD version of Windows).
*If you use STEAM there's a simple way to re-install Steam from within the SSD version of Windows while keeping all the games on the Hard Drive (Don't forget to copy all relevant Save Game data to the SSD "Documents" folder.)
Summary:
Long story short, use one copy only of Windows on the SSD. If space is an issue, Games and larger files should all be on the Hard Drive.