Unfolding the Mysteries of Drupal Messaging with PHPMailer and SMTP

This is a working document and I am just getting started compiling data from multiple sources. I have been confounded by the lack of support data and documentation surrounding the use of PHPMailer and the Messaging module for Drupal and I hope that this post starts to clear this up.

Drupal Module Home Page: Messaging

PHPMailer Provider: phpmailer.codeworxtech.com

Questions I hope to answer:

Why use PHPMailer and the Messaging Module?
What are some of the problems I have encountered?
Best practices when customizing the class.phpmailer.php file.
 

Online Resources
Great tutorial (Not Drupal Related, but gives basic details regarding how the PHPMailer works)