Phaser 3320 Manual Feed

I have a problem with the phaser 3320, the users have plain white in the tray but they also require to print on special paper using the manual feed. I have enabled bypass mode on the web page but when they put paper into the manual feed it still only uses the tray, the only way around this at the moment is to remove the tray or empty it. I thought it should detect any paper in the manual feed then use that first??