Creating an Application
If you want to make a standalone application for usealice.org, follow the instructions on this page.
Configuration
Most of alice can be configured through the web interface. There are two dialogs that can be used to alter the configuration, Connections and Preferences. To bring up either of these dialogs click the gear icon in the bottom right hand corner of the page.
Connections

The Connections dialog is used to add or remove servers. It should be familiar if you have ever used an IRC client (and I assume you have.)
The only difference of note is the "Avatar" field. This field sets your realname, which Alice abuses (or misuses) for avatars. If a user has an image URL or an email address as their realname, it will be displayed as an image next too their messages. This feature can be disabled in the Preferences dialog.
Preferences

The Preferences dialog can be used to set options that are not connection specific. You can toggle the use of avatars, timestamps, and notifications. You can also edit a list of highlightable terms.
Notifications

If you get a message with your nick in the body while the window is not focused, a notification will apear if you are using Chrome or Fluid (a SSB for OS X.)
You can add additional terms to highlight in the Preferences dialog.