Does the customer ever see what is put into this box.
For example can I put “awkward so and so but have agreed to waive postage” safe in the knowledge that the customer will never see what I put here.
No, the customer will never see what you put into the “Order details” field in the back-end, it is for administrator only. If you would like customer to see some information you should put it to the “Customer notes” field on the “Order info” page.