You typically turn down the start amps, end amps, and up and downslope controls when using a pedal. The whole point of the pedal is to give you control of those things on the fly. The one thing that is used with the pedal is pulse, and even then for slow pulsing some people do that with the pedal, too.
Pulse settings usually fall into two ranges. Slow pulse around .5 to 4 pulses per second is used to maintain a steady feed and travel rhythm and can be done with the pulser or pedal. Higher pulses from 30 and up are used to help control heat, and focus the arc to narrow the bead. Jody has some videos on pulse on WT&T that show the effects when welding near an edge. A lot is a personal style thing, and pulse is not needed for most welds. It's just another tool that can help in some situations. The best way to get a feel for the effects is to get some scrap and practice with different settings. The pulse time on and ratio of pulse amps to background amps effects how much heat reduction you get and the frequency affects how much more focus you get. Jody's rule of thirds is a good starting point. 33Hz, 33% background amps, 33% pulse time.
http://www.weldingtipsandtricks.com/...ent-pulse.html
Long arc, short arc, heliarc and in-the-dark!