You can leave internal order notes on your sales orders. It is not visible to your customers and can only the viewed by control panel users.
If you want something to predominately stand out on an order, you can add a sticky note which is displayed brightly on the order screen.
To add a sticky note from the Neto dashboard, navigate to Sales Orders > View Orders.
Click on the order you wish to edit and on the left hand side, select Add Sticky Note.
Scrolling down further on the order, you can also leave system internal notes to the left of the order totals which is also handy for ongoing notes about the order.