Also, how can I change the background color of the buttons on the site? Like the Ok, Submit, Cancel buttons?
Those will just be in the CSS. Look in the CSS for submit.button or just .button.
As for changing the background colors for the menu headers, you can always simply download the current template code that's on your site by heading to the Advanced Layout Options and clicking "History", then right click the last deployed layout and doing a "save as". From there, you can modify various paths (like the path for the javascript).
In most cases, an update won't break your custom layout. Retaining backwards compatibility is a priority whenever Advanced Layout Options are updated (usually, it's just adding new commands).
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It's all in the reflexes.