I have an ASP.NET (2.0) web application that shares no code with DNN and has a distinct web.config file. During development, it has lived happily side by side with DNN in two virtual directories in the same IIS website.

e.g. http://localhost/dotnetnuke
and http://localhost/mobilephoneapp

Now they are ready to be deployed to a production webserver (IIS 6.0). I want DNN to be run through the site root and the mobilephoneapp to be run through a virtual directory off the same site:

e.g. http://www.company.co.uk  <--- this is dotnetnuke
and http://www.company.co.uk/phone  <--- this is the mobilephoneapp app

My problem is, with this setup, the mobilephoneapp uses the web.config of
dotnetnuke, because dotnetnuke is in the root of the site. How can I
make them live as distinct applications again, but with the addresses specified above?

OK thats clear. Both of those options are feasible however not what I ideally want. Is there any way that the DNN site's address can stay as http://www.company.co.uk if the phone application lives under http://www.company.co.uk/phone (maybe some kind of redirection that happens at the server level that is invisible to the browser .... I am making this up, just wondering if it can be done)?

I don't know whether this helps because of missing infrastructure though it is a real world solution.

I would use an ISA Server as front proxy.

So I would run my webserver with a virtual server dotnetnuke and a second virtual server appserver/phone. Now I would publish them using ISA. All request going to www.company.co.uk/phone will be transfered from appserver/phone, all other request  will be transfered from dotnetnuke.

Every other front proxy which is able to seperate its requests based on the path will do its job.