When you say that you are 'setting them up' on Publisher, is that just within 'Page setup'? That only affects the page design, not the printer settings.
Print settings are accessed via the printer's driver. Click File>Print. Then click 'Properties'.
Exactly what you see from there on varies between printers but you'll probably have to click on something like 'Page setup' and then 'Page size'. Once you've selected the relevant settings, click 'OK'. (If you'll be doing a lot of printing with those settings, click 'Apply' and then 'OK', to make them your default printer settings).
Chris