The index page for the dark theme is 'index-dark.html'. If you put this file in the 'theme' folder in your project directory and call it 'index.html', your app will always start with the dark theme. The file can be found in the 'deployment\web' folder in your project directory after running once from the Modeler.
Look under prioject/settings and then the tab Model. There you can set your default theme. New themes can be downloaded from the appstore or create them (see the wiki about creating own themes).