" after a stress test it increased fps by 10"
I doubt it...
I moved the topic to this one, because Processing in NetBeans (or in Eclipse, etc.) isn't "Another Language", but it is still Java... That's basically the same language, that's why I doubt you will gain a big speed gain, unless you fixed something bad in the original, .pde code. IDEs like NetBeans provide other advantages, like auto-completion or debugging facilities, but not really speed gains.

Apparently, you don't know what happens in the PDE when you hit Run.
Processing takes the code in the editor, and runs a pre-process phase: it alters some syntax variants, like #AABBCC changed to the equivalent integer value, int(var) changed into parseInt(var) and some other minor "fixes".
Then it groups all the code of all the .pde files under an umbrella class (named after your sketch name), which is the one extending the PApplet. And it adds all the needed import statements.
Actually, when you export a sketch, you can see this Java code, in the generated .java file. It can be used to locate the lines mentioned by runtime errors...

So, all the so-called global variables are actually fields of the created main class. All the classes you can make are actually inner classes of the main one. That's why we have some restrictions, like not being able to use static fields there (unless you make the class static too), but also gain some facilities, like all classes seeing the "global" variables, etc. By skipping a class level, Processing makes Java an almost procedural language, perhaps easier to learn, without the heavy baggage of OOP.

Back to your problem, you can actually reproduce the structure I described in NetBeans, by putting all your classes inside the main one.
Or you can follow the Java design philosophy, with more or less separated classes, communicating via accessors (or public variables which is OK for small programs). But as you experienced, it complicates a bit the coding.

Maybe not a big deal, just an organization one, but in netbeans is there a way to put all the classes inside the main class without having a very long single class tab?  In processing you could make several tabs which would be separate pde files, but in netbeans it appears that all classes in one would result in just one "tab" and a much larger amount of code condensed together.