It took me some time to figure this out, so to those of you who are as dumb as me, here is how you do it:
- First, go to your blog setup, and make sure Markdown is the default formatting option. In Moveable Type, you need to select Edit Configuration > Preferences > Default Text Formatting for New Entries;
- go back to ecto, and choose Window > Accounts, select the blog you want, and click Update cache in the toolbar.
- In my case, I also changed the ecto preferences, in Editing, the default mode to HTML. If you are going to use Markdown, you might as well change all the HTML Text colors in that pane to black.