If you want to mark a specific item Out of Stock, navigate to the Menu page on the Online Ordering dashboard, select the category on which the item resides and then click the Sold Out button next to that item.
When you click the Sold Out button, two options will show immediately:
Back in Stock, which will make the item available as soon as you enable it, and
Back in Stock Tomorrow, which will schedule the item to be back in stock tomorrow morning.
If you don't click on either one of them, the item will remain out of stock until you chose one of the options above.