Printer Settings

I support a 750 user Enterprise Network. We have quite a few printers connected to our network via.. Extended Systems Print servers.
There are a total of 3 settings when configuring users to print. 1)The settings on the Printer. 2)The settings forthe Printer Properties(In Windows) 3)The Document settings in Word, Excel…. From time to time we have users that print to the wrong trays for no apparent reason. I would like to know which of these settings take precedence over the other two, and which settings cause the others to be ignored?