I'm not a big fan of the themes in Code Editor and would like to create my own custom theme (Sublime has some great ones). Whats the best way to creat my own custom theme so it doesn't get overwritten with updates to JCE?
There isn't currently a way to use a custom theme without modifying the existing themes (you can choose from a small selection in Editor Profiles -> Plugin Parameters -> Code Editor), but I will add an override option in the next update, where you can add a theme.css file to a media/jce/css/codemirror/ folder to use instead of the selected theme.
Just because you're not paranoid doesn't mean everybody isn't out to get you.
You can now select a "Custom" option in the Code Editor Theme, and then use a codemirror.css file in media/jce/css/ to set the custom theme, for example, a theme based on Eclipse (not the use of the "cm-s-custom" selector to coincide with the "Custom" theme selection) :