It’s OK to use your third party payment provider. AFTER, you’ve collected payment from your third party provider, go to Shopify and create a CUSTOM ORDER. In Shopify: Create Order + Add a CUSTOM Item (can be from your product line, but just retype the product name along with price etc. + Click add item. Then, click “COLLECT PAYMENT”, scroll down and “MARK AS PAID”. Marking the item as already paid AVOIDS Shopify from charging you a fee. You’ll still be able to see the items listed among your orders and you can still fulfill the orders through shipping. Hope this helps. If it doesn’t call Shopify. Their reps are usually very helpful.
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