At the subwoofer, turn your subwoofer volume to zero. Set the crossover at 80hz. Make sure your phase is at 0 degrees. Same at the Yamaha setup which you should see in the setup/speakers section. Make sure you have the speaker 'ohm set correctly.
Start some music or something you are familiar with and gradually increase the subwoofer volume at the subwoofer until you like it. If it sounds "not in accord with the speakers", turn the phase on the subwoofer to 180 degrees. Repeat the listening exercise.