Using Carousel without module
You can do this on the theme level. 

Your obviously going to want to setup the content using the CMS so will take the form of nodes.

You can then use a process function to determine what content type you are on for applying your script, for example...

function YOURTHEME_preprocess_node($variables) {
   if ($SOME_NODE) {
      // Add JS plugin...
   }
}


You can then create template files for node or specific fields in that node with markup that the plugin can manipulate.

node--[CONTENT_TYPE].tpl.php


To be honest, take Clives advice, use the modules, thats what makes Drupal what it is.