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Latex is just the typesetting engine - it creates the document, what you then do with that is upto you. It can be outputted to PS. Since you have CUPS set up, you can send the PS to the printer on the command line:
lpr -Pmyprinter -o sides=two-sided-long-edge filename.ps
where 'myprinter' is the name of the printer as setup by CUPS.