The sensor bar needs to be horizontal with the group of 5 leds at center of screen. I don't think the board being an inch higher thatn the monitor will make much of a difference because you'll calibrate the gun anyway.
I use mine behind tinted glass with no problems.
Here is what Aimtrak says:
IR Gain
This setting controls the "brightness" of the internal IR sensor. Normally this can be left alone because the gain is automatically set, but you can disable automatic gain control by checking the Disable checkbox.
When automatic gain control is disabled, you can set the gain to one of 5 values with the slider. There are very few situations where you may need to do this, but one such configuration might be where the LED PCB is located behind a tinted glass screen. In this case the gain might need to be increased.
If the Disable checkbox is checked, the slider still functions but will be over-ridden during use. In auto mode the slider moves on its own.