Homebrew PCBs

I have had success making single sided boards with Press-n-Peel blue 
but am unsure about making two sided.
Is there a trick to properly aligning the sides of a two side PCB 
when ironing on traces with Press N Peel blue? 
I figure I need to do one side and drill so there is a reference on 
the other side but then how to hold it perfectly in place for the 
iron process.
Any suggestions???