How to create a uniform look for the header and navigation menu with this plugin

Hello,

Thank you for making this plugin. It works great, except that I cannot make the header appear uniform across my entire site. Is there a way I can do that while using this plugin? The main menu not only looks different visually but it also has different links on them when I am using two different themes. It seems I can only edit the menu links of the active theme so the inactive theme has their own set of links.

Any help is appreciated, thank you.