Homebrew PCBs

Thanks to all who replied! I just noticed something, when i was first 
trying to plot double sided pcbs, I would first plot on paper then 
try to lineup the alignment holes i made on to the paper. However, 
even though i put the paper down on the holes, the plotter would 
always print the holes to the left on the pcb. I am using Eagle Cad 
if that helps diagnose my problem.