If you're planning to apply partial payment transactions made on Shopify to your bank account connected on Xero, you may set this bank account on the 'Apply received payments to this bank account' option on the app Invoice Preferences section.
Once you select a bank account here, then Reconcile.ly will attempt to create a payment within Xero using that bank account against the order. This is handy if you are accepting partial payments on orders and would like to view the balance in Xero.
However, if you are applying these payments, ensure, when you are reconciling, that your match against the 'payment' created and not the invoice.
If you do not want payments to be applied, just make sure to keep the field set to 'Do not apply payments'.
Note: the 'Apply received payments to this bank account' setting will appear only if you have selected 'Created' as the time you would like to export the invoices to Xero.