So each most packages I find point me to git hub and the install directions invariably say:

Open the Sublime Text 2 Packages folder
clone this repo

Is the exactly the same thing as simply downloading copying the directory into my packages folder via my OS?

or is there some built in mechanism within Sublime text for doing this?

It’s the same as downloading and copying, except if you clone the repo then you can use the git command-line tool to automatically update the plugin.
In general, though, I recommend doing all of your package management using wbond’s excellent Package Control plugin: wbond.net/sublime_packages/package_control. Easy to install, easy to use. You never even have to open your packages folder.