How to mark an item as private
If you want to have an item that isn't visible on your checkout for any reason, then you can mark it as private.
You can still use private items as bonus gift cards in promotions, and you can still sell them directly by targetting your checkout to include the item: How to show one item (or group of items) in your checkout
Here's how:
1) First, find your item and click on it to edit:
2) Next, you'll want to scroll to the bottom of the page, to the Advanced settings section and select (change) next to Publicly available:
Once you've selected that, you can scroll down a little further, to see the Visibility, limits & schedule section.
Once you've done that, you can save the item, and that'll automatically hide the item from your checkout.