Calculate Shipping Later for Custom Packaging

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Our store is a packaging manufacturing company. We make custom-made packaging for a lot of different industries. We are currently offering 1 product (in multiple sizes) available for Shopify checkout, our bags/pouch packaging. We have changed our checkout process so we only accept a 50% deposit, which is customary in manufacturing. We then will invoice and bill the customer once production has completed, normally at this point is where we also charge for additional shipping costs. However, it appears that Shopify wants to be integrated in the shipping process. Is there a way we can get around this and just charge shipping as we normally do? we'd like to be able to enter the shipping charges manually as well because we use a 3rd party freight forwarder who tells us the rates and we just relay those costs to the customer. 


Our normal process goes as follows: 

Customer places order > Pays a 50 % deposit following an invoice sent by our team > Production begins > Production completes > We send a final invoice for remaining 50% + Freight > Customer pays and product ships 


Thanks in advance

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