Some customers may opt to pay for a bunch of invoices through a single online payment. This could be for various reason, primarily to save the bank fees spent for each individual transaction. If you were to go to each individual invoice and record a payment it would be a hassle. Zoho Invoice lets you record this payment at one go and specify which invoices have been paid for, among the customer's unpaid invoices.
If your customer has deducted the tax before paying you, please check the "Has the customer retained the tax?" option Enter the breakup of amounts paid for the invoices Click the Save button
Zoho Invoice FAQ