I place the thermometer about 1" off the substrate on the cool side to measure ambient temps. The probe goes on the glass on the warm side. If you know the lamp is going to have an affect on the temp in this location then maybe the cool side isn't as cool as you think.
I have another question of my own though...Can anyone tell me why my cool side substrate temp measures 80 when all of my ambient temp readings are 82 on several thermometers throughout the room and the tank? Weird, but I don't think I need to worry too much about it.