the standard flow would be to enter each invoice and register the payment for the required amount, but this generates a payment complement for each invoice. In order to have a complement that has all the invoices it is necessary to do it from the bank reconciliation, the flow is the following one:
- create an account statement in the bank journal
- in a line put client, amount and form of payment
- publish the statement of account to go to the reconciliation.
- of the registered payment add the invoices and modify the amounts according to the need.
- validate the account statement and force the CFDI
- with this the invoices will be partially paid or paid depending on the case.
- in one of the invoices see the payment to force the stamping
With this the XML of the payment complement is generated with the ID of the document of the invoices to which the payment is registered.

I leave a video of @Marco Alejandro Morales (mams) making the flow

video