I have a web application that comprises the following:
Your application will only use the config entries in the web.config file. You can put dll config setting in the web.config file as long as they are structure properly. My example is VB specific using the My Namespace, but it gives you the general idea.
In the configSections paret of the config file you will need an entry:
Then in the applicationSettings part of the config file you put the entries for each dll:
False