This new Atmos I don't know much about but the Yamaha receivers I've helped set up seem to make you choose between a 2nd zone or the extra front high surround. So I suspect you need to go into your set up menu and designate from 2nd zone to whatever the other choice is for surround.

They don't give you enough channels for everything so you have to pick how you want to use the last 2 channels, either 2nd zone or extra surround channels. Yamaha's manuals aren't the easiest to understand but if you aren't able to find this option Yamaha is usually good about answering email inquiries.