Q. regarding progs on ssd and hdd

I recently built my first computer, and all went well! I recieved a free 60 gb SSD with my asrock extreme6, along with buying a 2tb hard drive.

I put the OS onto the SSD along with bf3, this is all I honestly need on there.

What I don't understand is why when I install programs into my 2tb HD the files dont install into folders, some do but most don't. They install outside instead, so I'm now stuck with 3 or so programs all mixed together...

Along with this is a few other programs that, even though I installed steam on my 2tb HD there seems to be steam files within the SSD?

I've searched through the internet, but to be honest I'm quite the novice and all the information baffles me, wondering if there is a simple fix to this? any guides etc.

Thanks in advance!