I've been able to place files on my IIS server using Microsoft.Web.Deployment code:

```
DeploymentSyncOptions syncOptions = new DeploymentSyncOptions();
DeploymentBaseOptions sourceBaseOptions = new DeploymentBaseOptions();
sourceBaseOptions.ComputerName = "localhost";

DeploymentBaseOptions destinationBaseOptions = new DeploymentBaseOptions();
destinationBaseOptions.ComputerName = ComputerName;  // remote host
destinationBaseOptions.UserName = Username;
destinationBaseOptions.Password = Password;

 DeploymentObject deploymentObject = DeploymentManager.CreateObject(DeploymentWellKnownProvider.IisApp, deployDirectory, sourceBaseOptions);

 deploymentObject.SyncTo(DeploymentWellKnownProvider.IisApp, RemoteFolderName, destinationBaseOptions, syncOptions);

```

It seems like all this does is create a new folder underneath an existing web application. If I go into IIS Manager, Right click the folder I created, and click "Convert to Application" then I get the behavior I was looking for. Does anyone know how to do this just using the Microsoft.Web.Deployment package?