I'm not sure what your accountant is doing to get the data into quickbooks. I'm guessing they are connecting to the database, so if you get it into the database they should be able to get it into quickbooks.
Is the selected program and notes getting into the database correctly? If so, then the accountant should be able to get it into quickbooks. I'd need to know how the quickbooks integration works to figure out why it doesn't work properly. The first step is to make sure all of the data is in your database.