Notes will show up if your client views a meal plan on Eat This Much (both web and mobile apps), and when you create a PDF or email out of a meal plan. If you copy a meal plan, the notes will be copied with it.
Select the three-dot icon at the top of a day, or to the right of an individual meal, and select the Create note option.

Type in your note and save, and then you'll see your note appear directly in the meal plan.

Once you've added a note, you'll see an Edit Note option in the menu that you can use to edit as needed.

You can also switch to your client's accounts to leave notes directly on their Planner page.
Meal Notes will persist when regenerating a meal (and even when regenerating the day or week). If you'd like to remove a note, simply click it, highlight the text, delete the text, and save it again. If the note is blank, it will not show up anymore.