Hi @jeremykp if your concern is only payment split, I think the easiest way for you is:
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Shopify Payment take the payment from your customer.
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At your backend, you’d better calculate the amount you need to send to the non profit organization on a daily/weekly/monthly frequency. It might need a communication with your bank.
If that’s not possible, you can build your sale channel app to completely take over the payment processing or checkout process on your own way.