Using a custom Android manifest.
In your game.project file there is ability to define a custom manifest file for Android. You may find you need to change some things in the default manifest to fit your project.
If you do need to make changes you must still start with the one shipped with Defold as it is a kind of template.
You can a copy in your Defold folder. Look for it in:
plugins\com.dynamo.cr.bob_1.0.0.[version]\com\dynamo\bob\bundle\resources\android\AndroidManifest.xml
Copy and paste this into your project folder, define it in game.project (found in Android section), and then make any changes you need to.
Keep in mind when you do download updates for Defold you may need to update you Android Manifest file! So pay attention to that and check with a diff compare tool and then pull over any changes into your custom one.