Once you've connected the Shopify integration to Springboard, you must fulfill sales orders in Springboard - not Shopify - for the integration to work properly.
If you fulfill a sales order in Shopify that will trigger the synced order to cancel/close in Springboard and will not capture the sale or remove the inventory.
After the sales order has synced down to Springboard, you'll need to distribute the items and fulfill the invoice. Check out this article to learn more about how order fulfillment works in Springboard.
Springboard will use Shopify's payment service upon order completion to charge the customer's credit card and complete the payment. Payments in Springboard will be reflected as "Shopify payments".
If you've already fulfilled a few sales orders on Shopify, we recommend recreating the order in Springboard then use a custom payment type as a place holder for the customer credit card (already charged in Shopify).
Check out this article to learn how to create custom payment types in Springboard.