Why the bank deposit does not equal sales
A gateway may batch several days of payments, deduct processing fees, hold reserves, include refunds or settle on a different date. Matching the net bank deposit directly to sales can hide those components.
The role of a clearing account
A clearing account acts as an intermediate balance. Gross customer payments are recorded into the gateway clearing account. The later bank settlement moves the net amount to the bank, while fees and other adjustments explain the remainder.
Gross payments − refunds − gateway fees ± adjustments = net bank settlement.
Keep gateways separate where it helps
Stripe, PayPal, Braintree and other methods can settle differently. Separate clearing accounts make it easier to investigate a balance without mixing unrelated gateways.
Offline methods need different treatment
BACS, cash on delivery or trade account terms should not automatically receive a gateway payment in Xero. The invoice may need to remain unpaid until the bank transaction is reconciled.
How ClearCommerce supports the workflow
Payment mappings are user-controlled. Each source method can point to the appropriate Xero account and choose whether it creates an invoice only, invoice plus payment, contributes to a daily summary or is skipped.