Is there a good resource that explains how PD's FFT works with some explanation of the theory and applications?
try http://www.parasitaere-kapazitaeten.net/Pd/fft_und_pd_en.htm - it pretty much covers exactly what you're looking for, although if you're completely new to doing fft you may have to expand your theoretical knowledge using some non pd-related literature to really understand the topic.
tom