I have a single screen with a side drawer and I got it working across the app by adding layout to the options of the center screen and not the root:
Navigation.setRoot({
root: {
  sideMenu: {
    id: 'sideMenu',
    left: {
      component: {
        id: 'SideDrawer',
        name: 'yourApp.SideDrawer',
      },
      visible:true,
    },
    center: {
      stack: {
        id: 'App',
        children: [{
          component: {
            id: 'HomeScreen',
            name: 'yourApp.HomeScreen',
            options:{
              topBar: {
                leftButtons: [
                  {
                    text:'Menu',
                    id: 'sideDrawerToggle',
                    active: true,
                    visible: true,
                    display: true,
                  }
                ],
                background: {
                  color: '#000',
                  },
                title: {
                  text: 'Your App',
                  fontSize: 18,
                  color: '#fff',
                  fontFamily: 'Helvetica',
                  fontWeight: 'bold', // Available on iOS only, will ignore fontFamily style and use the iOS system fonts instead. Supported weights are: 'regular', 'bold', 'thin', 'ultraLight', 'light', 'medium', 'semibold', 'heavy' and 'black'.
                },
              },
            }
          },
        }],
        options:{
          topBar: {
            background: {
              color: '#000',
              },
            title: {
              fontSize: 18,
              color: '#fff',
              fontFamily: 'Helvetica',
              fontWeight: 'bold', // Available on iOS only, will ignore fontFamily style and use the iOS system fonts instead. Supported weights are: 'regular', 'bold', 'thin', 'ultraLight', 'light', 'medium', 'semibold', 'heavy' and 'black'.
            },
            backButton: {
              visible: true,
              color:'#fff'
            },
          },
          //add layout here
          layout: {
            orientation: ['portrait'],
          },
        }
      }
    }
  }
}});