It may be subjective, but I think that having an overall view of what a library offers you can help. It's not necessary to know everything in details, but it's still good to know what you can do with it. (there may be a time issue). You could try to read Prototype and Scriptaculous In Action.
I just recently got turned onto Prototype myself. I found the three articles on the Tips and Tutorials page very useful, and also very easy to follow. I'm sure you'll want to take a look at the Ajax article, if you haven't already, but I highly recommend you read How Prototype Extends the DOM as well. It's a quick read but goes a long way towards explaining Prototype.