Is there extra charges to receive payments from invoices?

You can apply QB Payment account to integrate with your QBSE.

https:// quickbooks.intuit.com/learn-support/en-us/bank-transactions/what-are-the-fees-for-quickbooks-payments/00/535052

You can use a 3rd party processor to accept ACH payments for free. But you have to migrate the data manually as it only supports QBO.