When reconciling payments in Xero received via Ezi-Debit to match to your SimpleClinic invoices, you have two options:

1) When you are reconciling in Xero, you have the option to select Adjustments -> Bank Fee.

2) You can contact Ezi-Debit to change your settlement terms to gross full amount. This means they will deposit the WHOLE amount without taking out the fees, so you can go and reconcile your payments as you normally would with any other merchant settlement. Then, at the end of every month, Ezi-Debit will take the fees separately for the transactions processed. 
This is the most common way we see pracs handling Ezi-Debit settlements.