How to Make an Omeka Plugin

I am currently working on an omeka project, where users will have the option to use our header or use their own.
I've looked at:
- Which is an ok start to doing this, but it doesn't show how to implement the plugin files into the index.
In other words, how would I tell the plugin to place necessary files where I need them to go? Such as php files, css files, etc.
Am I missing something?