Solution:
It took me quite a while to figure this out.
Let us say you want to use Verdana as the default font. Here is what you can do:

1. Open contents.css and change the font tag:
font-family: Verdana;

2. In the application/page where the output will be published, add this style:


That's it! Now you have change the default font successfully. This works for the font size as well. I just finished developing this question2answer site, [url=http://banatbanat.com]بنات بنات[/url], which utilizes CKEditor and this tiny issue kept me awake for two days!