How to dynamically add an alert banner under Header

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I've built a plugin that allows merchants to customize a banner along with some text. I want to dynamically add this banner under the header of their store. What's the best way to do this dynamically? I don't want to have merchants add these tags into the theme manually. What's the best way to find the header tag in the theme to inject some HTML dynamically? Should I be using a script tag? What selectors should I look for and are these selectors reliable?