I wanted to get a post like this on the forums in-case anyone else is looking for the answer. Be aware, I'm a complete and utter novice at web development. Here are my tips for installing some common extensions:
That is WebFaction's official docs, and they do a good job of explaining the process - once you know what process you need help with.
My question was how to install a site analyzer like Piwik or Open Web Analytics, etc. The page above explains it. The rest of my post explains my process.
This took me about 2 hours to figure out (more if you count wasted attempts last week). I'm sure there is a better file on this, but I wanted to add this to the community Q&A for anyone interested.
The index.php file is what triggers the installation. Sorry if the end of this post seems rushed.
This question is marked "community wiki".