But to try to answer your question, I can point you to Part 1-5 of the
audio library tutorial, which is pages 6 & 7 in the PDF. That part of the tutorial shows how to change the volume with a pot, while the audio library plays a song from the SD card. The full source for all the tutorials is available in Arduino by clicking
File > Examples > Audio > Tutorial.
In the walkthrough video, you can hear the volume change smoothly, no "zipping noise" (still have no idea what you mean by this). Skip to 6:17 in the video, where you can see Alysia turn the pot and you can hear the volume change. This is how you can change the volume without any problems.