In the provided assignment content, it is suggested that for a complex project with bidirectional connections between JSP forms and Servlet action classes, grouping all classes into one package according to their type (view-related or controller-related) can make it easier to track each class. Additionally, distributing code work into separate files using JSP files for view sections and Servlet class files for controller sections can help in tracking data flow from one form to another and one class to another. The assignment content also highlights the importance of understanding design patterns such as MVC (Model-View-Controller) and EJB (Enterprise JavaBean).