The first thing to take note off is that Reconcile.ly doesn't import every order paid using Shopify Payments into your Xero. Instead we operate on the principal that 'Shopify Payments' is a customer of you (they hold your money) and all your orders / Shopify customers, are customers of 'Shopify Payments' (they collect the money on your behalf).
This means you only need to send one invoice to 'Shopify Payments' for all the orders a payout contains.
We also have support to send any orders that used other gateways straight to Xero. You'll see this option in settings.
The following diagram illustrates this concept:
Reconcile.ly creates these invoices (or credit notes if its negative), doing all the hard work of working out net amounts, fee's, adjustments, refunds and tax exempts sales etc, so that once you match the payout to the invoice during your reconciliation, all of your accounts will be credited or debited correctly.
If you are using other Apps that simply import all orders into Xero, this may complicate things. Reach out to us if you have any questions!