I want the boot drive to be different than the system drive

Here's the situation.
I originally had a windows 7 system and I installed all my programs to the one hard drive I had.
Recently, I decided to add an ssd and get windows 8.
I want ONLY THE WINDOWS 8 FILES on the ssd.
This is not the problem, since I installed a clean version of windows 8 to the ssd.
However, if I choose to boot from the ssd all of my programs are giving me an issue.
(Also, they do not show up in the "uninstall a program" thing.)
On the other hand, if I boot from the original hdd, to make it the system hdd, it boots windows 7 instead of windows 8.

Can I boot from the ssd but use the hdd as the system hard drive?
I've seen plenty of people trying to do it the other way around.