GoDaddy Application vs Manual Install I would like to setup a Drupal site with my existing GoDaddy Hosting Plan.

Do you recommend using the Drupal Application (provided by GoDaddy) or installing Drupal (core) manually into the hosting account?  Why?
Assuming this is what you are talking about Godaddy Application for Drupal

I would highly suggest to install Drupal on your own. That version is two releases behind with Drupal 7.34 addressing another recently found security issue with HTTPS websites.