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.
Each plugin (track) offers different configuration options. To find out what options are available you will need to read the documentation for the plugin in question. A list of these plugins is available here.
The config file is a Javascript object and, as such, must be properly formed. Object properties must be separated by commas, as must elements in an array. A common mistake is to add a comma after the last item in an object or array, or to miss a comma between two entries. More information about formatting can be obtained from JSON.org.
This is a consequence of the same origin policy, a security mechanism in modern browsers that prevents cross-site requests. To get around this, you will need to configure your server as a reverse proxy. For more information, see configuring a reverse proxy.
I strongly recommend using Firefox with the Firebug extension enabled. This will quickly identify the exact source of errors in most cases. If you can't quickly resolve the problem, please contact me and I will see what I can do to help.