The most common logic changes will likely occur in business objects. However, it's likely you'll also make changes to the ASPX and CodeBeside pages.

Although it's possible to subclass ASPX and the CodeBehind pages I don't think there's a lot of value in this functionality for front end code. Changes made to these files should be tracked and if you do perform an update you need to back up your copy of these files and copy them back in.

In short changes made to the ASPX code are going to be one-way changes that will modify the store's behavior and functionality with no hope of consolidation in future updates. In order to use future versions of the store you have to merge your changes into newer versions manually.