Here are a couple of things to check before installing Reconcile.ly
Reconcile.ly sends a invoice per payout and/or order depending on your settings. Make sure your Xero plan supports Invoices and are not limited. We recommend having at least the 'STANDARD' Xero plan.
If you have other apps that send orders to Xero, you should turn these off to avoid duplication.
Your Xero organisation currency should be the same as your shops base currency.