Splitting Order Payment for Print on Demand between Manufacturer and Owner

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I operate a print on demand apparel manufacturing business that manufactures and fulfills for several customers who are on Shopify. The order management and processing is no problem with our shipping platform integration, however, the real pain comes in during invoicing and payments. Right now we collect the order information and send an invoice at the end of the month. It's tedious, manual, and complex. It takes hours at the end of each month and is too easy to miss items or make mistakes. Not to mention the loss of time value money and the risk of not being paid. (I've been stiffed by two customers now which has forced me to change my policies.. sigh, lesson learned not to assume all people have integrity)


I would like to create an app that I could essentially associate all SKU's that I fulfill with a manufacturing cost that would be deducted upon placement of an order and sent to our account? E.G. (Hoodie is sold for $60: 40$ goes to me the manufacturer and $20 goes to owner) There would also be other complexities to consider here including shipping and fulfillment fees and how that would be broken up. In general, we need a way to automate this and also ensure I am getting paid. 


If the split payment was too much I would settle for an auto invoicing app that extracts the order information, compiles it into a report, and then sent the invoice to the customer on a set interval. This would help reduce a mountain of paperwork and more consistent cashflows.

Does anything out there like this exist or do I need to go the custom route?