The easiest way to start is to just copy the contents of the templates directory after cloning/downloading the rally-app-builder repo to your local machine. Then you can tweak the html files in the deploy directory to include any other custom app markup.
You may run into some weirdness with App SDK 2 depending on what ExtJS layouts you're using. I haven't tried to do what you're doing, but apps usually are designed to fill their window and I know we have run into some interesting issues in the past trying to combine them with other content.
The other option is that you could just re-implement the html from your other apps right inside your SDK2 app. That way you'll be playing within the ExtJS layout system, and you won't need to use custom output templates with the app builder either.
this.add({ xtype: 'component', html: '<div class="app1">html here from old app1</div>'});
this.add({ xtype: 'component', html: '<div class="app2">html here from old app2</div>'});