EBS compares your estimates to the actual time spent on tasks in order to generate better predictions of how long future tasks will take you to complete. So, for example, if you are generally an optimist and under-estimate how long tasks will take you, EBS will learn about this over time and take that into account when it's predicting ship dates. A more complete discussion on what EBS tries to do and how it works can be found over here.
To answer your question though, generally you should try to enter your best guess at an accurate estimate when you start working on a case and then leave it alone. You can adjust the estimate if you like, but if you fairly consistently over or under estimate tasks, it's almost better not to (given how EBS works).