Some programs have custom Print dialogs. This may make it difficult to locate the Two-Sided printing option.  For example, Adobe Acrobat Reader DC has its own Print dialog that will appear.  Clicking Printer... at the bottom will allow you to bring up the Print dialog that most Mac programs will display.

If you receive a prompt like this one, click Yes.

You will then be able to specify that you want to use the Two-Sided option.  Options available may vary based on the printer you are using, as well as if you are using AirPrint or a CUPS printer driver.