Since Airprint has no tray choice you are pretty limited.
Assuming both trays have the same paper loaded the same way, tray priority is the deciding factor when it requests standard paper. But some of the apps make their own decisions too
I believe that I have already set the manual feed to the lowest priority ( highest number ) or do I have that backwards? It doesn't seem to matter what those setting are.
Apple does not provide tray selections in their protocol, they only use "whatever the default tray is".
So the only option is to set the tray you want Airprint to use as the default for any job that isn't specified, which can be done via CWIS > Properties > General Setup > Paper Management > Tray Content & Settings and swap the priority of tray 1 and 2
It appears that AirPrint is only using tray 1. This appears to happen on all of our iPads regardless of the application we are printing from. Is there anyway to force AirPrint print jobs to use a different tray.