To do things like manage sub domains, creating domains, etc. control panels usually provide an API.
I have experience in PLESK panel. PLESK panel provides XML based interface for you to programatically achieve admin tasks.
You have to read the documentation for the control panel you are using - I am sure they offer this.
You also have to consult your hosting provider to see if they allow XML RPC remote calls. Mine didn't and I had to specifically ask them for this permission for a payment.
Remember, you wont be able to use IIS management classes available in .NET to manage IIS directly because of permissions. You would need to use API provided by the control panel.