Tried reinstalling Win7, installed a second copy instead

I upgraded to windows 7 a little while back and wanted to reinstall it, start fresh, yada yada... When I ran the win7 disks yesterday, rather than replacing what I had, a second copy of win7 was made and now it automatically boots to the second copy. Unfortunately, the second copy has virtually none of the software and features that it should. However, I found them in a folder entitled windows.old, but I'm not sure how to use them. Any help is appreciated.
 
I have Windows 7 upgrade disks, not original Windows 7 installation disks. Will that be a problem for your suggestion?
 
No

No, it shouldn't. But have qualifying installation media just in case. It'll tell you what counts as this if you need it.
 
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