I think your problem  is that you can not design  your
application; you need assistant of a software engineer
if there is any accusable for you.
But for a short answer if you are designing a j2ee
application (web based) you can read j2ee patterns
available in www.javasoft.com home page.
And if the application is not j2ee then one of the
simplest ways to do this is using MVC pattern (Model
View Controller).
In this architecture you have a view which do all GUI
thing(object and classes,…) and a model which contains
all business logic object (persistence objects,
workers, utility classes, etc) and then the controller
controls the way messages are passed from one to
another,
If you need more assistance in designing your software
send me more info about your project and I will try to
do more help.