Pictures would help...
Are these ancient hang on back heaters or something? Almost every heater sold today is submersible (completely). They have a 'fill line' on them for two reasons. One, it is requried by Canadian Law, so if sold in Canada it must have that on it. And two, that's the minimum amount of the heater that must be underwater to prevent the glass from cracking.
So what will happen? As said above, you risk the glass cracking because of the heat differential.
If these are submersable heaters with the suction cups on them, just lower them down further, or change their orientation so they are completely under water (for example 45 degrees, or horizontal).