This was the confusing part when I first ran couchapp to create a new app, I couldn't really see where the "entry point" of the app was. In the hope that it might help someone else I'm going to present a quick overview of the default setup.
index.html
The index.html page is a static attachement, and the user starts by requesting it with their browser.
It has some small amount of static HTML, part of which creates a div for the javascript to put the data in.
Either inline, or in an included file, there is a small bit of javascript that will initialise the couchapp.
By default this will use the div with the id items, and will attach an evently widget to it.
evently
The evently widget that is attached will then either have an _init event, or a _changes event, either of which will be immediately run by evently.
This event will usually make a couchdb query to get data to transform to HTML and present to the user (see part three for how this works.)
Once that data has been displayed the user any combination of evently widgets or javascript can be used to make further queries and build an app that works however you like.
Previous installments
See part one, part two, and part three.