Right way to change encoding settings

Hi!
When I encode footages I have to differet ways to change encoding settings - one is AME's settings panel. Second is Codec options. I'm confused - where must I change settings, must they be the same in both windows, or what's "primary" options window? Please, explain!

Ok... But in that case, what settings are "primary", have a priority?  Those who are in codec options window or in regular AME settings window?

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