Can I set it up so that gross sale proceeds are deposited into my bank account and then the Shopify fee is separately debited from the bank account? This is how I had it set up with Elavon and it was much easier to reconcile the bank account.
In your billing settings, make sure the option to use your Shopify balance for billing is turned OFF. Then it will charge all of your Shopify, App, and Shipping fees to your card/bank account.