I would like all the tabs like "Files, Tickets, Discussions" to become highlighted in some way to let staff know the this section has info in it. Where do I get started?

Sorry I'm very new to aC what files do I edit? I'm still trying to figure out the file structure.

System just collects tab names and their URL without checking if there are objects present on the pages. Because of that tabs are no "aware" of data they display. Code responsible for displaying tabs is located in wireframe.tpl:

{if isset($project_tabs)}
<div id="tabs">
	<div class="container">
  	<ul>
  	{foreach from=$project_tabs->data key=current_tab_name item=current_tab name=page_tabs}
  	  <li {if $smarty.foreach.page_tabs.iteration == 1}class="first"{/if}><a href="{$current_tab.url}" {if $current_tab_name == $project_tab}class="current"{/if}><span>{$current_tab.text|clean}</span></a></li>
  	{/foreach}
    </ul>
  </div>
</div>
{/if}

Path: /application/activecollab/moduls/system/layouts/wireframe.tpl

Behavior you requested can be implemented, but it would require good understanding of the system in order to be done properly (per project counters for every type, caching to keep things as fast as possible etc). We do not plan to introduce such a feature at this point, but we'll consider it for one of the future versions.