I am using consolibyte library to sync data between MySql and QuickBook. Other data is being synced successfully but I did not find the Custom Fields. I have to sync only two three things Customers, Items and Invoices. Where the Custom Fields are being stored in MySql?
Custom fields are pushed to the qb_dataext
table.
Note that custom fields are NOT fully implemented (the code is in beta) so don't expect great support.