Basically, a plugin is a class which extends the original functionality of Handsontable.
If you wish to make your own Handsontable build, it's a good idea to choose the internal approach.
This way you'll simply need to include a customized handsontable.js (or handsontable.full.js, see the difference) to your website.
However, if you want to add a new functionality to the Handsontable without making your own build, and you don't mind linking more files to your site, you can go with the external approach.
Regardless of the chosen approach, you can access any plugin's instance by calling:
handsontableInstance.getPlugin('nameOfThePlugin');