Depending whether the payment was a deposit/pre-payment or an invoice payment, will determine how it is reconciled.
If the payment is for an invoice then Xero should match the payment with the invoice, if it is for multiple invoices, you can click the match option and match it with the appropriate invoices.
To handle deposits/pre-payments through a bank transfer, we treat it the same as an in hand payment, by where we create a receive money transaction and use our bank transfer clearing account.
- Pre-Payment is taken in EVOPOS and credit note is uploaded to Xero using bank transfer clearing account (this increases your clearing account)
- Payment comes into the bank feed
- Payment is reconciled by using create receive money transaction and using the bank transfer clearing account (this reduces your clearing account and increases you bank account)
This allows you to reconcile the payment before the invoice is created.