Settings are in the web configuration. Therefore, in your ARM template, you just need to add another resource (next to the site resource) as follows:
{ "apiVersion": "2014-06-01", "name": "web", "type": "config", "dependsOn": [ "[concat('Microsoft.Web\/sites\/', parameters('siteName'))]" ], "properties": { "virtualApplications": [ { "virtualPath": "\/", "physicalPath": "site\\wwwroot", "preloadEnabled": false, "virtualDirectories": null }, { "virtualPath": "\/virtualApp", "physicalPath": "site\\wwwroot\\virtualApp", "preloadEnabled": false, "virtualDirectories": null } ], // other web config settings ie "phpVersion": "5.4" } }
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