Configuration questions I can't seem to find answers for

I have search the forums and read the documentation but I can't seem to find answers to some questions. As a new user of CKEditor I obviously have a bit of a learning curve on it but hopefully the community here can help me out a bit.

I have created an instance of the editor using the jquery adapter. See code below:

$(document).ready(function() {
   var config = {
      //uiColor : '#577390'
      //templates_files : 'templates.js'
      //customConfig : 'myconfig.js'
   };
   
   //use jquery to build the editor instance
   $('#editor1').ckeditor(config);
});

The editor builds great and in its default state works. All of the examples I can find to configure the editor use the

CKEDITOR.replace( 'editor1',
    {
        toolbar : 'Basic',
        uiColor : '#9AB8F3'
    });

naming and editor access syntax. How can I access the same properties and settings using jquery's simple $ access to elements?

Secondly I tried in the example given to pass in the config array on creation and I cant seem to get the templates.js and myconfig.js to load. I'm confused on the path that should be given. Are the paths relative and if so relative to what? My files are in many different directories for organizational purposes so i really need to know since they are a lot of includes on pages in other places.

Thanks in advance and let me know if I need to clarify anything in my post.