Joel you use the rod to initially measure zero and then you change the rod to the depth you want to achieve. By rotating the turret and setting the screw heights you can plunge to intermediate depths before you rout the final depth. As Pat suggested the measurements on the rod are crude and the turret can have excessive play so precision can be hard to come by.
Someone I consider a master woodworker once told me that a master woodworker is not someone who never makes mistakes. He is someone who is able to cover them up so that no one can tell.