not sure what "big and complex" means to you and how experienced you are.
you can use different pde files / tabs in processing to order and structure your code.
putting classes and functions to different tabs already helps a lot.
if its getting bigger and much bigger you can switch to another IDE like eclipse for example

http://www.learningprocessing.com/tutorials/processing-in-eclipse/
http://wiki.processing.org/w/Eclipse_Plug_In

See also http://forum.processing.org/topic/subfolders-for-pde-files
In the past, I also suggested to be able to make libraries as uncompiled files, always automatically joined to a project requesting them, without going the hassle to put them in a jar file and allowing fast iteration to debug them, but it hasn't been done yet (if ever).