Hi Grant and welcome to Beans Community 🙂
Styling with CSS is ok but you might be able to make use of some the UIkit variables instead of overwritting the CSS. If structural changes are needed, you could make use of Beans HTML API or potentially WordPress custom menu walker if you want to completely re-write the menu HTML.
Could you post a quick wireframe of what you want your menu to look like so that we can point you to the right direction?
Thanks,