If you've set net orders to come in as final orders, payment must be collected outside of Shopify via bank transfer, QuickBooks, PayPal, or another external method.
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If you've set net orders to come in as drafts, you'll be able to manually edit the order before invoicing your customer. You can add shipping, adjust taxes, and set your payment terms before collecting your payment.
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You can manually add shipping for the order by clicking ‘Add shipping or delivery’ in the Payment section of the draft order.
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You’ll be able to select one of your store’s standard shipping rates, or create a custom shipping rate. Click ‘Done’ to add the shipping rate to your draft order.
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You can ensure that taxes are being added to the draft order by clicking ‘Estimated tax’ in the Payment section of the draft order.
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Select ‘Charge taxes’ to have taxes calculate and apply for the order. Disabling ‘Charge taxes’ will prevent taxes from being charged.
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You can also make specific customers tax exempt with a setting on their account page. Open the customer account page, find their customer settings and click ‘Edit Tax details’
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Select the ‘Don’t collect tax’ option. This will make it so that taxes are never calculated on that customer’s draft orders, or for their regular orders through your standard checkout too.
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Click ‘Payment due later’ to set a specific due date for the payment.
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You’ll be able to select the length of payment term, and the issue date (the date when the payment term will officially begin).

If you’ve set Payment Terms, you’ll see the ‘Create order’ button appear. This button works to complete the draft order, which will move it from the ‘Drafts’ section of your admin to the ‘Orders’ section of your admin. You’ll be able to send the invoice or collect payment from the finalized Order Page that is created. There will also be options to perform different actions like marking fulfillment, or putting the order on hold. This step is only necessary to complete a Net Terms order that you’ve added Payment Terms for.

Click ‘Send Invoice’ at the bottom of the Payment section.
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This will open a popup where you can customize the message that will be sent to the customer. You’ll be able to review the message, and send the invoice. The customer will receive your custom message, and will see the payment terms date that you’ve set for their order.
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If you’ve already contacted the customer independently and are ready to collect payment via credit card you can use the Collect Payment button. If you’ve collected payment outside of Shopify, you can use this button to mark the order as paid after you’ve collected your payment, too.
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