We have an order form and wish to add several additional fields such as delivery date, message, etc. Are there instructions on how to do that anywhere?
Not specifically. Usually these things are done through the my_changes (or similar) addon and use the cscart_order_data table to store the extra data. Some people will shortcut and just add the fields to the cscart_orders table but that can be risky down the road.
Generally you would use several hooks for 'update_order', get_order_info, delete_order, etc. to manage the data. You can look at one of the other addons like reward_points or rma to see how it's done.
Alternatively, you can hire a developer to do it for you. As with most things, the more you want to 'administer' the data the higher the cost.
Internal notes can be leaved in the "Staff notes" field on the order detail page. If you want to send message to the customer, just enable communication on the Addons tab on the same page.