Have you had a chance to read this series:
and more specifically within the series:
Hope it helps
Yes they are, you can put both your plugins AND doPlugins code into an extension and scope it to your site catalyst tag.
Plugins are the standard Adobe plugins that they support out of the box; we pretty much use them all in our s_code.js.
Here at my company, we heavily rely on doPlugins to rebuild data before sending off to Site Catalyst.