Connect to HDMI 3 (ARC) from your A/V receiver. That's the only connection you should be using. If you want to use ARC because you really must use the 'smart' features built into the TV, then you likely need to have HDMI CEC enabled, which may cause other headaches and issues.
There is no obvious reason you can't adjust picture settings across all the HDMI inputs. You may have to select 'manual' configuration for color instead of one of their pre-canned setups, but that's nearly impossible to figure out without having the TV in front of me.
Manufacturers can't even both to show the actual back of their displays in their user manuals any more, so helping others is becoming nearly impossible unless you actually own the exact same model.