Where to include javascript instances in drupal
To Add any js file to your Drupal site , a good way is to create a custom module and add your js file there.Following points may help you.


Create one custom module of yours. Useful Link. https://www.drupal.org/developing/modules/7
In your module , create one folder name js.
Add your js file here.You can copy paste your js file also here.
Now in yourmodule file the following code to tell drupal about your js file.

function YOURMODULENAME_init(){

 drupal_add_js(drupal_get_path('module', 'YOURMODULENAME') . '/js/yourjs.js');

}

At the end enable your custom module.You are ready to go.