Deploying multiple asp.net sites under the same folder

[Dan Avni]

I have a web site built with ASP.NET based on the dwamish books
sample. The site has a few DLL's (façade, business rules, DAL and a
DLL for configuration loading and logging) that it depends on and
(obviously) a web.config file.

We also need to create for this site a WAP site. So we started a
Mobile Web Application and created it using the same n-tier DLL's

Both sites on the Application_Sta rt on global.asax file call a
function which has these 2 lines
System.Configur ation.Configura tionSettings.Ge tConfig("Applic ationConfigurat ion")
System.Configur ation.Configura tionSettings.Ge tConfig("Tracke mConfiguration" )
The web.config file has a section with these names and the names of
the classes that implement the IConfigurationS ectionHandler

The site works perfectly and there are no problems when installed
separately.

However, this is my problem: The desktop site is installed on the
production server on a separate SITE. I now want the WAP site to be on
a WAP folder under the desktop site

e.g.:
The desktop site is at www.desktopsite.com
The WAP site should be at www.desktopsite.com/WAP/

the problem is that when I either put the WAP folder under the wwwroot
of the desktop site OR point to it using a virtual directory the WAP
site suddenly stops working (in both cases I define the WAP folder as
an IIS application)

The problem with the site is that suddenly it does not read the
web.config file (or at least the TrackemConfigur ation part of it)
And therefore I do not have the sites settings and everything crashes.

If I simply move the files to another location on a different site on
the IIS the WAP site works perfectly.
What is the problem? Can't I have an asp.net web site and under it in
a different folder another asp.net web site?

Thanks