Depending on your browser, Ponyhoof may or may not auto-update by itself.
If you use Google Chrome or Opera, they will auto-update extensions automatically, so you don’t need to do anything.
If you use Firefox, then Firefox will handle extension auto-updates according to your Firefox settings.
If you use Firefox and use Greasemonkey or Scriptish, they may or may not auto-update Ponyhoof, depending on your settings.
If you use Safari, you must install updates manually, due to Apple restrictions, only extensions that are installed from the official Safari Extension Gallery can be auto-updated.
Regardless of what browser you use, you will get a counter next to Ponyhoof Options, and an update message in Ponyhoof Options when there are new updates.