You can absolutely change all of these things.
There's two places you'll want to check- in Word/Excel/Powerpoint/Outlook if you plan to use the Nitro Office plugin to convert documents, and the Nitro 11 PDF printer preferences (for whenever you are printing to PDF).
For the Office plugin, go to the Nitro Pro tab in the Office program. You'll want to uncheck "Prompt for filename".
To change the paper size, turn off prompt for filename, and anything else for the Nitro PDF Printer, you'll want to go to Control Panel, Devices and Printers, and right click on Nitro PDF Creator (Pro 11). Choose "Printer Preferences".
Prompt for filename is on the first tab, Default page size is on the second tab Pages. There's Custom Forms if you need a paper size not listed there.
Hope that helps!