Log in to the Joomla admin panel: http://YourSite.com/administrator/
Click on Components -> JCE Administration -> Configuration
Scroll down to Formatting and set Use template CSS to NO
Put the path of your template CSS file into the Use Custom CSS field ie templates/YourTemplateName/css/style.css
The thing is now you’ve got a big long list of styles you’ll probly never use, so cut and paste the ones you want into a new css file (style-jce.css) and point the custom CSS field to it: templates/YourTemplateName/css/simple.css