>Am I right in thinking that the .jar file will contain .class files and not .java files?
>If so, how can I modify the applet after the Jar has been created?
You like... keep the source for that case
>Also, do I store the images in the Jar file?
With applets its optional, with webstart its a must. Btw it doesnt has to be the same jar. You can use one for code, one for images, one for sounds... etc. The benefit of this approach is that you can change them individually, which means that users dont need to reload that much again (only the changed jars).
If you want to create jars which arent double clickable (or change the classpath or something like that) you can just zip the files with some everyday zip application and change the extension to jar.
Some simple image loading example can be found here:http://kaioa.com/k/jarimage.jar
(doubleclickable/src included... usually you dont include the source... mind you)