IMHO keep thing simple. organizing something well does not means to make it complexe.
what's a java ( and also true for most languages ) project ? a source directory, a build directory, some ressource files & some requiered files/libraries that's all, maven will just make thing more complexe.
my opinion about IDE is the same, keep thing simple, I ve used JCreator for severals years now and always being very happy with it but any IDE/editor should/must to the JOB ( as a side note : all my java coworker have now all switch to it few months after I get into my new company and would never come back to netbean wich is damnly slow to compile (and even slow on executing
.. ) and produce tens of unneededs/obscure files and tends to freeze/crash some times.)
so you say you dont really know about build structure ? there is nothing to know more than what you already know clicking one button have to produce a destination working directory (without extra file that are not needed) from a source directory, that's all , and this destination directory or parts of it will be sent later for validation and than for production, nothing more.
also keep in mind that's may be better if anybody can still work on your project or make few modifications without having to use the same tools as you, and for that keeping the project clear is the key.
so here is my final advice : until you plan to make cross language compiling, I dont think you need any specific build tools. Using any specific IDE features may make your project linked to this IDE forever.
nowadays, lot of tools tends to make things appears complexe when they are not....
EDIT: about ant ? hum.. I dont think that your project will become a day more complexe to compile than something like "javac ... -cp jogl.jar ... @sourcesfiles" so what's the need ?