Ha! I just discovered the solution to part of the problem. On the printer's configuration menu (on the printer itself, not in the software utilities) there is setting that will allow it to print from Tray 1 if there is media in Tray 1. Here are the steps, in case anyone else needs the info:
On the printer, press the menu button
select Configure Device
then System Setup
then Manually Feed Prompt
then Unless Loaded
Press OK
That allows it to pull from the manual tray automatically if there is media in it.
But now I need to figure out how to get it to default to Tray 2, or to automatically pull from Tray 2 if there is no media in Tray 1.