phpVMS can customized to fit your VA's look and feel. The templating is powered by Laravel Blade. To understand skinning and changing templates, study the Laravel Blade documents, and then the below will make more sense.
app.blade.php has 3 sections that are extended by the templates.
@section('title')is the page title, and shows up in the title bar
@section('content')is the main content for the page
<script></script>tags when extending this section.
A few good resources are:
Laracasts is a great resource for learning the ins and outs of Laravel.