When exporting to markdown Manuscripts does not make any semantical distinction between the title and headings (e.g., it uses setext-style syntax == for the title and atx-style # syntax for the headings). I was wondering if this problem could be solved by resorting to yaml-styled metadata blocks, such as:

title: The title
author: Author
affiliation: Whatever
email: email@email.com

This has two advantages: (a) both pandoc and multimarkdown recognise the syntax, and (b) it allows to include more information such as author list and affiliation, email, and even abstract and keywords.