Awesome, after being on here for 4 months I finally figured out how to write toots with markdown formatting:

Toots can be written in three source formats:

• Plain text: toots are treated like in vanilla Mastodon, and are not formatted
• Markdown: toots can be written in Markdown, as understood by Redcarpet
• HTML: toots are written directly in HTML (but sanitized to strip any unsupported formatting)

You can write toots in Markdown or HTML from the glitch flavour by first enabling “Show content-type choice when authoring toots” in the “Compose box” tab of the app settings.

(from this page)