The printer properties you can think of a the default settings. The print settings within individual applications are personalized, for lack of better word, for that app. This enables, for example, Adobe to always print double-sided but leave Word printing on only one side. If you were to prefer all documents from any application to print on both sides (or any other feature), you could set the printer’s settings to do so. I know this isn’t a very technical explanation but thought it would describe the difference in a more basic fashion.