First, make sure that you have read through the page that I referenced earlier. That might help if you get stuck.
If your application is installed in IIS, delete the IIS application.
Then, in IIS you select your DotNetNuke application, right click and select Add Virtual Directory.
Locate the directory in which your asp.net application resides and select that. Give a meaningful alias.
So, if your DotNetNuke application is
http://mysite.com, and you give the asp.net application an alias of myaspapp, you should be able to visit your asp.net application as
http://mysite.com/myaspapp (I wrote this from memory, not from actually doing it, so I hope I got all of the steps.)