Two main activities in AndroidManifest.xml

The LAUNCHER intent filter is what determines what shows up in the app drawer/launcher. That is why you get two icons shown up.

However, you also set the DEFAULT intent filter, which sets the default Activity for the whole package. Since you set it twice, you get the problem of precedence of the first/latest registered. When you remove the DEFAULT filter, you will be able to start whatever you click on in the launcher.

In short, remove the following line from both Activities:

<category android:name="android.intent.category.DEFAULT" /> 

Yes, just mark two or more of your <activity>s as LAUNCHER within your manifest. In addition you have to set the android:taskAffinity attribute on both of your Launcher-Activities which specify the exact package and Activity to be started.

<activity android:label="MyApp" android:name=".MyApp" android:taskAffinity="com.example.MainActivity">
        <intent-filter>
            <action android:name=".MyApp"/>
            <action android:name="android.intent.action.MAIN"/>
            <category android:name="android.intent.category.LAUNCHER"/>
        </intent-filter>
</activity>


<activity android:label="Settings" android:name=".Settings" android:taskAffinity="com.example.SettingsActivity" >
    <intent-filter>
        <action android:name=".Settings"/>
        <action android:name="android.intent.action.MAIN"/>
        <category android:name="android.intent.category.LAUNCHER"/>
    </intent-filter>
</activity>