I grab a new noise sample for each light stage of noise reduction that I do--since you're changing the noise profile each time you run the NR, this seems to give better results.
The FFT size adjustment is on the "Advanced" menu of the Noise Reduction controls. Yes, it's the same idea as the FFT filter in the filter and EQ section. I won't embarrass myself by trying to explain Fast Fourier Transform (that would take maths well beyond my ability) but, at the simplest, it controls how Audition is sampling the noise you're trying to get rid of.
