Use a layoutview instead.
You could do for example:
var ContactManager = new Marionette.Application({});
var LayoutView = Backbone.Marionette.LayoutView.extend({
template: "#layout-view-template",
regions: {
menu: "#menu",
content: "#content"
}
});
ContactManager.layout_view = new LayoutView();
ContactManager.layout_view.render();
I never actually add regions to my app object directly.