you will have approximately 2 x component Video Inputs on the rear of your Yamaha Amp. These can be assigned to inputs not being used.
I would recommend using component, I don't feel you will see a difference in resolution between HDMI and Component as the ATV is really only a 720p product. It does allow a 1080p output via HDMI but restricts it's programming to 720p.
The benefit in going component is this will allow you to maintain all video Switching via the Amp.
Minimum Picture gain or massive convience gain.
You will also need to connect an Optical cable for audio and possibly assign the inputs on your amp to suit. oh and select component output on your ATV.
I agree with Warwagon, Component is the way to go in this situation. If you had more than one other thing, I'd say get an HDMI switcher, but at this point there's no need.