Thanks for the explanation. I do understand what you mean, I do need to record the order in Zencart as a paid order regardless of if I collect payment or not. I do now understand that I can use any of the payment modules you mention for this. I think the problem was that I didn’t understand how to do that through the storefront without offering one of the payment methods to my customers.
I do not wish to have any of these payment methods available for customers to use. So as suggested earlier I can hide the payment method by IP address. It might not be the perfect solution but indeed it will get the job done. When I travel and use other IP’s I will need to also change the hardcoded IP address before I can place a manual order.

Regarding shipping something to a customer that wasn’t paid; yes I do actually send free product samples/gifts to my customers sometimes. I guess I will have to charge $0.00 for these orders to be able to record them.

Super Orders and Edit orders are definitely great and very useful modules, I do see now that I can add Payment and Refund charges, I guess that is what you call processing a credit against the order.
One thing about Super Orders: I can’t split an order that consists of only one part number, for example I can’t split one order of 4 green T-shirts into two orders of 2 green shirts each. Not a big deal, I will just have to place a new order through the store-front instead of splitting it.

Thanks for the suggestions, I appreciate your help. I can’t say that this is the perfect way of creating manual orders but I guess currently it is the best and only way to do it.