I am not sure that you are understanding how form guides works. Form Guides leverage the XFA template design in Designer to allow you to have an alternate interface for collecting data. The structure of the guide is built in Guide Builder but the underlying definition for the template is in the XFA template in Designer. The only time that Flex Builder would be required is if you wanted to modify individual components or layout styles. So to answer your question build the form in Designer then use Guide Builder to bind the individual fields and objects to the appropriate panels.