We recommend that you always host your asp.net application in your domain's root directory. You can infact create a sub domain to host each of your applications. If that is not possible, you must open a ticket specifying which folder in your domain must be created as an application directory.
If you host a .NET or ASP application (that has a global.asa file), it must be hosted in an application directory. The root directories of all domains are application directories by default
