I am using web.config as well. 
As for the building ConfigFactory, try using this:
Code:
config = new Configuration();
            
ArrayList list = new ArrayList();
Assembly[] assArr = AppDomain.CurrentDomain.GetAssemblies();
for(int i = 0; i < assArr.Length; i++)
{
   if(assArr[i].GetName().ToString().IndexOf("Lib") > 0)
   {
      config.AddAssembly(assArr[i]);
   }
}
point is, that I separate logic and view (I am using maverick.Net - MVC) and all assembles containing Business objects and their DAO are called {something}Lib. Using this simple convention, I can simply map all BO without any additional config file.