Technically, you don't need to set it as a system app. The app downloads a driver into your phone. The driver you should choose is High Quality Audio. You can choose Super Quality Audio because the GS3 is dual core, but I've tried that and it overheats the phone and causes it to lag. After installing the driver, tap on menu and change the UI Setting. I have mine set on Expert. Gives you a lot of options. Spend some time going through each setting. It'll make your headphones/Bluetooth speaker sound glorious.
The thing with flashing ROMs is that you have to install the driver through the app after each flash. Most of the time after opening the app after flashing, it'll tell you to download the driver. Sometimes, it won't. That means you have to go to Menu>Uninstall Driver, restart the phone, open the app to download the driver, and restart your phone again. This app is worth it.