Let us assume that you have associated the Authorize.Net payment gateway and have to get paid for 5 invoices. Let us also assume that the invoices are for $100 each. Whenever you receive payments online or record payments manually, you may select the Deposit To field as a bank account(Example: CITI) that you have set up in Zoho Books.
Once your customers pay for the invoices through the Authorize.Net payment gateway, the money will be held up with Authorize.Net for a short interval after which it will be deposited into your CITI bank account as $500.
Now, to match the five customer payments to a single deposit:
With the bank rules, this can be further automated leaving much lesser work for reconciliation.