If you are new to Prototype and Scriptaculous then this book is your ideal starting point as this book clearly describes both how to use prototype and scriptaculous as well as giving you some idea of how the frameworks actually work.
I'll start by admitting that I have never looked all that closely at Prototype since I consider the 120k library to be far too big to use with web pages where the entire page including all files should never be bigger than 80k given the speed at which most people currently connect to the internet. This review isn't about Prototype itself though but about a book that teaches you how to use Prototype once you have decided to use it.
As you would expect from someone actually involved in creating Prototype, this book provides a detailed coverage of all of the methods that the framework provides that you are ever likely to use, how to use them, and what to use them for. Reading about all of the fantastic tasks that this library allows you to perform has convinced me of how useful that using these frameworks actually is. Now if only I can find an environment to run it in that isn't dependent on downloading web pages from the internet or alternatively a way of compressing the framework down to a more reasonable size (like about 5k).
A very impressive book for anyone wanting to learn a really easy way to convert web pages into interactive applications.