That's a pretty broad question so unless ya ask something more specific all I can do is tell you what I do.
If I want to sample something from a song on my ipod, I have a cable that goes from a stereo 1/8 jack to two 1/4 jacks, I plug the headphone out of the ipod into the audio in jacks on the Fantom. Then I press "sampling" and queue up the part I want to sample on the ipod. Then I start the sampler and hit play on the ipod. Then I use the sample editor to trim off anything unwanted at the beginning and end of the sample. Then I save it to my PCMCIA card, or use it in a rhythm kit, or assign it to a pad, etc.
Hope that helps.