I am using Eclipse with Java 1.6. I was wondering what the preliminary steps were to set up the Stripes framework. (What do we do with the .jar file?)
I don't understand the basics of the framework, as I have thoroughly searched for a clear explanation (other then the Stripes website).
That sounds to me like you are missing the fundamentals of java web development. Maybe you should read the servlet chapter of the Sun JEE tutorial, especially the bit about web modules:
Sun JEE Tutorial: The Web Tier
Basically you neet to create a WAR archive, where the stripes jar lies in the directory WEB-INF/lib. To wrap the WAR, you can either use IDE methods (e.g. in eclipse) or specilized build tools like Maven (here is an old but still valid Article about web development with maven, there is also a good online maven book from Sonatype, but I wouldn't know where to point you at, there's not really a web tutorial in there).
The official Quick Start Guide provides a step by step guide to get you up and running with Stripes (the guide covers basic configuration and the development of your first Stripes application).
If you don't understand the instructions, then I suggest to follow @seanizer's advice and start with the Java EE tutorial on the web tier first. You really need to get basics skills before going further. Don't put the cart before the horse.
There is an really excellent short(!) book on Stripes that covers all aspects:
Stripes: ...and Java Web Development Is Fun Again
by Frederic Daoud (Pragmatic Programmers)