An Anno-J 'instance' is a website that you can visit to use the application. For example, the Salk Epigenome site is an 'instance'. Using an instance of Anno-J is simple; just visit the website using a W3C compliant web browser such as Safari or Firefox.
Creating an instance is a little more involved and requires website administration skills plus access to a web server (Mac OS X users: you already have access to the Apache web server). If you don't feel confident at this stage, then contact your local website administrator for advice.
If you are familiar with CSS then you can use it to style your instance of Anno-J. As of Anno-J 2.0, the GUI uses the ExtJS framework, which provides a fairly clean design. Although you may override these styles, it's not recommended as the ExtJS HTML structure can be very complex at times. However, you are free to apply any styles you wish to the tracks themselves.
Custom stylesheets may be included in the <HEAD> section of the instance's HTML page or in the instance's Javascript configuration object. The only difference is that sheets included in the config can be toggled on and off actively by the user.
This documentation is thin at the moment, but will be expanded on in the future. If you are proficient in CSS and wish to start designing new sheets, contact me and I will elaborate on how to get started. Generally, it's no more complicated than reading the documentation for a data source and designing classes to match the class names streamed down by the data service.