Hi Nicole - YAS,
For the payments where she doesnt raise an invoice, presumably these transactions appear in her banking section of QuickBooks if she has her bank account linked up. Alternatively she may upload CSV files at regular intervals. Both these methods work in the same way. Once you have the transactions in the 'For Review' section of the bank she should allocate this income as a Sales Receipt to be able to allocate a customer against it (the deposit feature will not allow you to do this).
For all the income that an invoice is raised for these can be matched in the banking section as normal.
I hope this helps if you have any questions please do not hesitate to private message me on here.