Changing the default printer settings
After you've logged onto your system, if your using KDE, open the application menu and search for Printing. In Gnome it's located under System -> Administration.
In the Printing window that appears, you'll see the printers you've installed. Right click on the printer for which you wish to change the settings and chose Properties.
In the Printer Properties window select Printer options.
Change Media size to A4 to set the default paper size.
Change Duplex to Long edge to set 2-sided printing over the long edge as default.
And change anything else you want to have as a default setting here. When you've selected your preffered settings, click OK and you're done.
Now every time you send out a print-job, doesn't matter from what application, it should print with the settings you've made here... unless you tell the application to print it in another way.