To create manual orders we recommend the following:
Create a 100% multi-use discount code in your Shopify store.  Keep it in a safe place.
Use your Shopify store to place manual orders. Create the design and add to cart just like a normal customer would.
When checking out use your customers shipping address.
Process orders as normal from the Customized app.
To make it even more streamlined you can store your frequent order designs as Templates.  That way your product design is already created in your Shopify store and you can make minor tweaks (i.e. personalization, colors) or order as is.