For a small site on a shared host, if I place the main DNN site in a  SUBDIRECTORY (like www.domain.com/dnn), and use a index.html to redirect it redirect from the www.domain.com location, what  negative consequences does it have with search engine rankings (eg google, yahoo,...)? 

The issue with most shared hosts, if you install an app in the root, then that app's config conflicts with deeper config files. So, I need to determine if SEO issues offset the hassle with the config.

The issue is if I place the program into the root directory, the entire ASP.net system picks up the configuration file in the root directory.  This causes no end of problems for other applications, eg. they use the DNN config.