1-Why cross over at all? The Cornwalls are known for great bass. Go full range to the speakers. Run from the Yamaha direct to the speakers.
2-Try without the sub and see if you are happy. I would be.
3-Pre-out on the amp should control sub volume. You may not hear much. Set the sub as low as it will go or see if manual mode will work?
That's the idea of a good sub match. It will just compliment the bass. You just might have more speaker than sub.