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 DotNetPanel
1. Login DotNetPanel
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 with the same name as actual directory.