One is an SSD where Windows 7 is installed as well as a few other programs and games that I want to be able to start quickly. I have another normal HDD that has my other (majority) of my programs and games.

I was just wondering if I choose the upgrade option (I know the risks), will Windows 8 still register the programs that are not on the SSD and are on the HDD? Or does it only register the programs I have on my SSD?