By default you can upload asp.net application to wwwroot folder and run website.

If you want to host asp.net application in a subfolder, you have to configure virtual directory for the sub-folder.

Please follow instruction below to create virtual directory in WebsitePanel

1. Login WebsitePanel

2. Navigate to hosting space -> Web Sites

3. Select website you want to host asp.net application -> Virtual Dirs

You can create a Virtual Directory (IIS application) with the same name as actual directory.