I'm using the digital output via my receiver and everything is working just fine.
Try connecting the subwoofer and speakers only through the optical sound output, on the back panel of the motherboard. Don't connect anything else, expect that because optical sound connect's everything combined together (subwoofer & speakers). Basically, you should one cable mounted to your motherboard.
Before you do that, it's necessary to install the Asus audio codec's as one of the first files because it's a bulky type (over 700mb, I believe), after you installed Windows. It shouldn't take long to install the codec, it'll reboot and then you should be just fine. Practically, you should be able to choose between the sound output's from the motherboard or graphic's card through Windows sound 🙂
P.S. Make sure you connect the optical cable after you installed the audio codec and subwoofer/speakers turned off.