@ciaramay – If you want to manage popups rather than pages you simply create popups the normal way and reference this guide https://docs.wppopupmaker.com/article/51-open-a-popup-from-a-wordpress-nav-menu to add it to your menu.
Alternatively you could automate the entire process, and instead of creating popups, create pages. This allows you to disable in the future and still have a working site. This also means each popups content will be accessible via the standard page url. IE an about page can be accessed at /about, or loaded into a popup using Remote Content extension. With that extension you make one popup and tell it to activate on any link on your site loading that link into the popup.
Either works well, one just requires less management :).
Hope that helps.