Bank Reconciliation and Cash Application

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Hi. We are currently working on an integration with Shopify and our backend ERP system for a client. We can bring in orders from Shopify, push inventory levels from the ERP to Shopify, push shipment data from the ERP to Shopify, etc. The issue we are running into is how to reconcile the payment and bank deposit.

Can anybody tell me if the amount Shopify deposits in the merchant account is net of the Shopify payment fee(s)?

Any recommendations on how other devs working with accounting software integrations have handled tying a payment made before a product has shipped to an invoice after the product ships?