I have 2 web.config files at root/ and at root/Web. I want that when I hit /Root/Web my application should load a certain set of settings from the root/Web.Config even though they are present in /root/web/Web.config
Any ideas where and what should I be modifying?
Yes, the way to do that is removing the elements in sub web.config that conflict with the settings in the root web.config.
If you need them for other purposes then you need to read whatever settings you want/need and apply them programmatically.
From MSDN: