If you find out that you can’t print to trays on a printer because all your print jobs are going to the manual feed, please try and do the following.
First, remove the trays from the printer and empty out the paper. Once the paper is emptied out, look and see if the latch settings on the tray are set properly for the paper size. If the settings are incorrect are not locked in properly, the printer will look for the manual feed instead as it assumes your paper size is larger or smaller than your print job requires.
This is a very useful feature to you (though you may not feel that way) as if the latches are loose so that the paper can move around in the tray, you will risk a paper jam when the paper if picked up at an angle. Also, if the latches are too tight, the paper will be lodged into the tray and can wear out the rollers as it tries numerous times to retrieve the paper and eventually show a misdeed/jam error.