When you use "Automatically Select" in the printer driver, it will select the paper source based on the size of the page you are printing. You can register different paper sizes for the main cassette and manual feeder.
The easiest way to do this is to create a custom profile (preset) and set it as the default.
If you select your custom profile and select "Always Print With These Settings" check box, the printer will use these settings unless you tell it otherwise.
Sounds like some overcomplicated procedeures.
Normally the printer feeds off the cassette, this is to be expected.
When user wants to use some special paper, he/she opens the rear tray and puts them there.
Now user still needs to manually select "rear tray".
But the logical and usual operation should be to prioritize the rear tray whenever it's loaded?