Question about Refresh/Reset with apps installed elsewhere

Hello everyone. It's my first post here so I hope it's in the right place.

My PC is approaching that state where the bugs are piling up (most recently, explorer has been choking a little on boot) and it's time for a refresh. I understand that process, but I have a two-drive setup: a 100GB SSD that serves as the system volume with certain other things installed (antivirus, graphics drivers, et. al.), and a 3TB harddrive that houses all my files, libraries, and installed programs.

As I understand, the refresh/reset will only affect the SSD. I have everything backed up just in case, but the process should only wipe the system volume. My question is this: how can I get the refreshed OS image to recognize everything I have installed on the HDD? For example, Steam is installed on the HDD along with a lot of games; how do I get Windows to recognize where it is and re-add it to the startup program list, whatever registries need to be updated, ect. without installing it all over again?

I know this might end up being a program-by-program task, and that's fine. But if there's a way to prod windows and save time and bandwidth, that would be great.

Thanks in advance!

Load or mount your windows 8.1 installation disk so it is visible from within your current OS
Then run Setup.exe
This will upgrade your current OS, keeping all files and programs.
Your current OS will be moved into a Windows.old folder od your SSD

That's not what I was asking at all. I already have 8.1 and I have no interest in changing my OS. If I use the built-in Refresh or Reset function, how can I get it to recognize programs installed on other drives afterwards?