Hi Melanie,
You can disable marker titles at the Maps Marker settings section under a tab called something like ‘marker list settings’. After that you can simply add the marker title(s) in the WYSIWYG editor on the edit/create maps marker page.
I’m sure though that the alternative solution to automatically show the marker titles in the pop-ups as well shouldn’t be too difficult to implement, for example when you base it on the function which does that already for the location.
Great plugin by the way, but the CSS code is completely messed up and all over the place – which is a pitty. Takes forever to customize it.