The default command to send printing jobs under linux is "lpr", and all the commands that comes with it. To configure some options by default, for example for my office computer, I have to set them in the file : ~/.cups/lpoptions. This is what I have : 
Default The_Printer_Name Binding=LeftBinding KMDuplex=Double StapleOption=1StapleLeft StapleSet=True
This will hence configure those option by default.
  • Binding : by default, put the binding ("reliure" (fr) ) on the left
  • KMDuplex : by default, print in duplex mode ("recto-verso" (fr)).
  • StapleOption : by default, staple once, on the left corner
  • StapleSet : by default, staple all documents.
NB 1 : Of course, I can modify all those options before printing, for example in acrobat-reader (acroread), or okular, or evince, or whatever I'm using. NB 2 : Those options may (or should I say "will") vary from one brand to another... (This is for a "KONICA MINOLTA bizhub C360 - 0" printer)