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You have two options to change the navigation button colour:
Either you edit your Site CSS. This is a Yola Silver feature for advanced users.
You can do it the way you mentioned: You can "hide" the default navigation menu and create your own custom navigation bar at the very top of your site's body section.
To hide your default navigation menu, you will not use the option to display navigation links in your navigation at all. So if you create a new page, you will never check the box next to "Display in navigation".
If you already have pages, you must take them all out of your navigation by going to the Page Manager and changing the green arrow to a red X for each page of your site, inlcuding the index page. Once finished, you will see that your navigation bar is gone.
Now you can create a sample page with your custom navigation menu. You can use the Custom Panel Widget to create a sleek navigation bar or buttons, then add text using the Text Widget, and link that text to the respective pages of your site.