Please share yourn site url.
So that i can check and provide you exact solution here.
This is Rae from Shopify. Thanks for reaching out with this question.
Can you please share your store's URL with us here, like @oscprofessional mentioned? That way, we can pull up your site to look into the menus further.
In the meantime though, there are a few troubleshooting steps I can offer.
As a starting point, when building the main menu on your site, did you include links in this menu that also belonged in the footer? If so, these links may give the impression that the footer menu is below your main menu. To check out the structure of your main menu, visit the 'Online store > Navigation' section of your Shopify admin and ensure that the links under your 'Main Menu' don't include any footer menu links. For more information on editing menus and removing menu items, check out this help document.
The Brooklyn theme also offers a secondary sidebar menu in the 'Header' section of the theme, so it's possible that the footer menu may be added to this placeholder by mistake. If this is the case, this will cause that menu to display under the main menu on this theme. To check if the footer menu is added here, just log in to your Shopify admin and follow these steps:
If you have another secondary menu that you would like to display under the main menu instead, feel free to add this menu here once you remove the footer menu from this field.
Let me know if this resolves your issue. If you're still having troubles, please reply here with your store's URL so that I can investigate further.
Looking forward to hearing back from you!