Hey John, welcome
For any of the acars, nothing has to be done serverside, except for FSFK, which needs FTP information. Any settings are in the local.config.php file, or in the app.config.php file. To change them, you copy them from app.config into local.config for them to take effect.
Also, with Joomla, the easiest is created a duplicate skin within phpVMS. Several VAs have done this, it just ends up being easier in the end. Some have tried using iframes, and I personally think iframes look ugly.
But the advantage with our way (create an identical looking skin as your Joomla install) is that you can customize virtually every single page to your liking. All the templates are in the core/templates folder, and to customize it, you copy it to your skin's folder, and it takes effect. You can also call any page into another page pretty easily, by calling the module then the function:
MainController::Run('pilots', 'index');
And that will show the pilots list... and you can put that anywhere (template, skin, etc).
Hope that answers some of your questions... if there's anything else, feel free to ask