Under Home > Set Preferences > General, you can check the "Show App ID Field" box (it's under the SuiteCloud Development Framework). Then on your existing custom objects, you can click the "Change ID" button. This will allow you to set the app id for each customization to match your SuiteApp project (com.netsuite.whatever). After you do this, your SDF deployment should recognize those customizations as part of your app.
Keep in mind, if you uninstall your SuiteApp later, those customizations will be removed even though they were there before you deployed your app.