Smaller FFT sizes will consume more CPU but have less latency (undesirable delay when you monitor a live signal, this doesn't affect already recorded tracks though). Higher FFT sizes will consume less CPU but have more latency. ZL mode attempts to give the minimum latency possible at the cost of very much CPU. So these settings don't affect the sound as such in any way, but if your computer gets overloaded with work, you may hear "glitches", which of course make the sound quality worse.