Project Shipment Invoices

We have recently started using Projects. Almost all of our Projects are for parts on the fly and have multiple Phases. We Invoice generally at the end of a Phase. Maybe it is Engineering Design of a certain area is complete. I would think that Customer Shipment is the best Invoicing method. The jobs under the Phase are all rolled up to the Phase Job. I was hoping to do a Shipment from the Phase Job but when you try and do that, Epicor says you cannot do a Shipment from a Project Type job.
Can anyone offer any suggestions.
I could setup a Milestone Invoice at the end of the Phase but then the costs don’t go through correctly to COS and it is an Advanced Invoice which I don’t need.
Thanks.