RTNovak:
The physical directory where you install DNN on disk does not really matter (you don't want to install DNN on a drive outside of the IIS server for performance reasons but that is another issue). The point is that it does not have to be at the physical root of the C: drive, it can be ten levels down, on drive Z:. What is important is that when you define the Web Site in IIS, you point it to the right physical directory, wherever it is, and then define the appropriate Host Header that goes along with it, like www.yourdomain.com. In that way, when an HTTP request comes into the server (IIS) for www.yourdomain.com, IIS will now where to grab the files from. In other words, the root of the Web Site (a logical concept) is wherever you point the Web Site to (the physical part). This of course also applies to SEO, after all, they can only access your site via HTTP just like the client browsers do (okay, more or less).
Edit: Forgot to address what I assume is your "redirect" page, can you elaborate on that? Why are you doing that?
Does this answer your question???
Carlos