There are different possibilities in order to create online markdown files.
Integrated FTP Text Editor
There are several FTP clients available for macOS (like Transmit or Cyberduck) or iOS (like FileBrowser or FTPManager) with integrated text editor allowing you to create and edit text files on your server.
There are several markdown editors available for macOS or iOS like iA Writer which let you create and edit markdown files. In combination with a FTP application you are able to sync these with a FTP server.