Sounds like you selected a specific paper type for your manual feed tray 1.
If you set the Paper Type for your manual feed tray to "Any" then the printer will automatically print whatever media is loaded without prompting you for additional decisions. Likewise, if you leave the paper type on Tray 2 as "Plain" and Paper Size as "Letter" then it will continue to print your normal sized print jobs from that tray.
If you are still having problems then shoot us your tray settings. We should be able to review and suggest a better configuration.