We have been able to connect MSCRM Online with QuickBooks Desktop and Online. Our standard template does integrate MSCRM Invoice to QB Invoice and MSCRM SalesOrder to QB SalesOrder. We add a field on these objects to trigger/queue it up for download to QB.
We can certainly provide directions if you want MSCRM documents downloaded to QuickBooks or other accounting packages like Dynamics GP.
We have built it on Java, and are working to make it available on Azure Cloud.