i am using drupal cms premium theme i am just looking to use javascript code to make additional features but it seems not compatible with my premium drupal theme only. although the same code is working with my free drupal theme which is making me feel that it is possible to make use of javascript code with drupal cms.

So what should i do to make it compatible with my premium drupal theme, is there any of the plugin or option which i need to make enable.

any suggestions.....

thanks in advance.