You have a bit of a chicken and egg problem and very likely a permissions problem.
An IIS application defines the root of an application (which has a web.config, and can be mapped to an appppool process etc...). An IIS application maps to an IIS directory which is a physical dir or maps to a physical dir (vdir).
You are FTPing code into that directory.
The first problem is creating an IIS application also requires very elevated priviledges which even if you could execute your code after FTPing, the application pool does not likely have and should not run with those permission.
The server administrator or hosting company should create the IIS application that maps to the folder that you're FTPing into. Either that or some configuration code/script/installer needs to be run on the server interactively by an administrator.
PS: There's one edge case where it may work which is if you're FTPing into a vdir which is where you need the IIS app created but it's under a root IIS application that's mapped to an apppool which is running as a very elevated administrator on the system (ill advised and likely not the case), you make a request relative to the root which would create an IIS app on the vdir where you FTPed. Very unlikely and you wouldn't want to run in that elevated environment anyways for something that's externally facing.
