Question about formatting and re-installing WIn 7. Have two HDs.

Hi guys. Got a quick question about formatting SSDs.

At the moment, I've got an SSD and a normal mechanical HD. I use the SSD for Win 7 and more important programs, and the mechanical HD for games, work files, music and less important programs.

I've set it up so that my SSD uses folders on my mechanical HD for the general library folders.

So I'm wondering how I would go about formatting my SSD and doing a clean install of Win 7 on it. I know I would have to re-install all the programs that were on my SSD before - thats no problem - but what about all the programs that were on my mechanical HD? Would the fresh install of Win 7 be able to run those?

thanks.