Once you have connected Xero to Reconcile.ly and confirmed your settings, starting from the next payout, we will begin sending this data to Xero in the form of an invoice.
To Reconcile a Payout (Orders placed with Shopify Payments), simply match this invoice against the payout in the bank feed.
To Reconcile separate orders being sent (Orders that didn't use the Shopify Payments gateway), then you will need to match against each order's invoice. E.g. A payout of $45 may require you to match with 3 x $15 invoices that were sent across.