Hi,
you could also create a custom field in Shopping cart item class and field with the same code name in Order item class in Modules - E-commerce - Classes.
Then you would need to develop only a custom control which would allow user to insert product note. Something like CartItemUnits.ascx.cs, which allows users to modify number of units in new checkout process.
The custom product note data would be copied from shopping cart tem field to order item field automatically when order would be placed.
Best regards,
Ivana Tomanickova