normally its only the front that is lowered or to be exact the forks dropped threw the triple tree's
Doing this gives you a steeper rake / headstem angle and gives quicker easier turn in, downside is you loose some stability but most are happy with the trade.
If your setting up suspension for motard you will find that it is normally set with less sag in the rear, thicker front fork oil and increased compression and rebound as compared to dirt.