Thanks Jonathan,
I wanted to know what you at ACF had to say about the subject. I understood how meta boxes work in the template file.
After thinking it over I remembered seeing the flexible layout add-on and wondered if it actually took care of the functionality I was looking for.
It seems as though it is! I develop a template part for each of the meta boxes I use. Then call them into the templates in the order decided by me and the client. Would I be able to use the same process but instead allow the client to change the order?
