Hi Ensign,
Have you got the auto feed activated for both accounts (square and current)?
Also have you tagged the sales transaction in your square account to sales invoices and the fees to purchase invoices? The difference between your sale and the square fee is the amount square transfers to your bank account. When it arrives in your current bank account (without a auto bank feed you do this entry manually or by uploading a bank statement) tag it as a transfer between accounts and select square.
Maybe this helps too
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