The webpage and driver are not linked in any way. The webpage is for jobs submitted on the webpage.
The driver will always print to the regular tray and the bypass is used when the job is programmed for what is in it, which typically is something abnormal to plain white Letter. So if you were to set the driver to print on "labels" and the printer bypass tray is loaded with Labels (Programmed as such) then the Auto select would work in the driver as long as Labels was set.
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??