To start using Markdown, go to Settings → Writing in your blog dashboard, check the box next to Use Markdown for posts and pages, and save.
I just enabled it for one of my test blogs and am happy to report that MarsEdit works perfectly for publishing with Markdown to WordPress.com. They mention that it’s best to stick to the “plain text” editor on WordPress.com, and the same is true for MarsEdit. You’ll want to stick with editing in “HTML Text” mode so the plain Markdown text can get to your blog without being wrapped in HTML generated by MarsEdit’s rich editor.
I wrote recently about MarsEdit’s ability to automatically convert Markdown to HTML before publishing a post. It’s worth noting that if you use the new Markdown functionality on WordPress, you probably want to avoid MarsEdit converting to HTML. This is because WordPress’s implementation of the Markdown feature does things “the right way” in my opinion, storing the original Markdown as the text of the post, so you can make further edits to the post by editing the original Markdown and not the converted HTML.
The only downside I’ve noticed so far is that when you download a post through the API from MarsEdit or from the official WordPress apps, the content is converted to HTML even though it shouldn’t be. The original Markdown does show up in the web-based WordPress admin panel. I’m going to report this as a bug and hopefully they will agree that it should be fixed.