Basically, waypoints are a method of insuring your units go where you want them in the way you want them.  It's not complicated, but most players don't like to give the time to them.  It's actually a lot quicker for scouting and bringing units around trees and such.  To perform waypoints, hold cntrl and right click some where on the map.  Still holding cntrl, right click another location on the map, repeat as desired.  White flags should appear where waypoints are performed.  When you are finished, let go of cntrl and right click on the last flag you placed.  The unit(s) will head towards the location, checking to each waypoint you created.  For worksites, you can place a waypoint flag on top of an unfinished building and the unit will follow your path and construct the building.  Even though path finding is increased in Rise of Rome, it is still not perfect, this is for those times when units just can't make it on their own.

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