JOGL doesn't have to be in any particular folder, so long as your code can find it at runtime. I usually put it either inside my program's project folder, or in a parallel project folder. For example, if you get the latest autobuild from http://jogamp.org/deployment/autobuilds/master/jogl-b436-2011-08-30_12-55-58/ and unzip it, you can just copy its "jar" and "lib" folders to somewhere inside your project folder.