Baitboy,

The pulse mode "pulses" the voltage on the wire between the natural voltage of the boat up to whatever voltage you have the box set to. Rather than a constant voltage on the wire. This will entice the fish by giving your wire a ramp up in power simlating an injured bait fishes voltage. At least that is the story that Elliott from Scotty USA told me.
I have used it and caught fish, but then again, I am still working the bugs out of my system. From what I am told, this mode is deadly for slow biting fish.

Scott