Although there is a markdown plugin available in Typesetter, it is not very pratical. Neither is the markdown plugin from CKEditor. So we can use Pandoc to generate the HTML source.
Under Cygwin, given you have the markdown text in the clipboard, you can launch following command to put the corresponding HTML in the clipboard:
getclip\ | iconv -f ms-ansi -t utf8\ | pandoc -f markdown -t html\ | iconv -f utf8 -t ms-ansi\ | putclip
For the source code to properly be displayed in Typesetter, launch the desired conversion with the -s option, and update the Layout setting from Typesetter with the content between the <section> tag (without the tag).
When using Pandoc generated HTML in Typesetter, there may be extraneous line breaks. To avoid this, add following line to the layout setting:
.sourceCode .cf::before, .sourceCode .cf::after { display: none; }