If you have a custom application such as NSurvey installed with your DNN site, it may be possible for you run the application in a virtual directory, however, PowerDNN will not provide technical assistance for the third party application.
If you ever have a custom, non-DNN application that you need running on your site, the absolute best way to handle it is to log into the control panel and go to:
System > [Domain] > SubDomains
and create subdomain that will only contain your custom application
PowerDNN will not provide free technical assistance for non-DNN applications.