I use the following code to create a app pool:
var metabasePath = string.Format(@\"IIS://{0}/W3SVC/AppPools\", serverName);
DirectoryEntry newpool;
DirectoryEntr
The other answers are better in your particular scenario, but in general keep in mind that you can use the appcmd tool to do this: https://technet.microsoft.com/en-us/library/cc731784%28v=ws.10%29.aspx. Specifically:
appcmd add apppool /name: string /managedRuntimeVersion: string /managedPipelineMode: Integrated | Classic