Help+Manual now supports importing Markdown files, both for creating new projects and into existing projects. See Creating an empty new project, New project with imported data and Importing data into existing projects for details.
There are no special settings for Markdown import as it is by definition a very simple format. The Markdown flavor (Daring Fireball or Common Mark) is selected automatically on the basis of the content of the file. A set of standard styles are used to represent the few Markdown formatting options.