My bowl doesn't sit firmly on the hookah, or goes all the way down to the tray.

Try turning the bowl as you wedge it firmly onto the bowl grommet. Be sure not to press too tightly if using a clay or ceramic bowl as you might accidently break the base of the hookah bowl. Occasionally, you may wish to use two bowl grommets instead of one for additional support and stability. You can also wrap a strip of moistened paper towel around the bowl grommet for a more secure fit.  As long as the seal is airtight - even if the bowl sits on the tray - the hookah will smoke normally.  Bear in mind, many bowls actually seal up inside the neck, and not at the opening of the neck.