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Download and install the QBFC installer from http://www.getgopher.com/qb. Run Quickbooks and open your company file. Then run Gopher 2006 and go to File | Quickbooks Link | Synchronize with Quickbooks. Go to the QB Customer tab and click "Export customers to QB". Then when you are ready to export invoices and payments to Quickbooks, you go to the "QB Invoice" and "QB Payment" tabs, respectively, and specify the date range that you want to export.
The first time you export your data to QB you will have to export your data from the "Tax Codes", "Tax Region" and "QB Pay Terms" screens. Gopher will tell you if there are any problems that need to be resolved before it can export to Quickbooks (e.g. if you did not export your tax regions).
It's always a good idea to make a backup of your Gopher and Quickbooks databases before synchronizing with Quickbooks.