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I currently have back orders enabled and I am attempting to set up my magento 1.9 store to be similar to my set up offline to avoid any processing issues/double charging. Right now my magento is set to charge up front for full order, regardless of backordered items or not. I want to be able to process orders as they are shipped. If ie: 2 shipments, 2 seperate charges.

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You can try to enable partial invoice for payment method. You should to declare $_canCapturePartial as true in model of payment method(s). After this you will be able to create partial invoice in backend.

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