The LED notification, if working properly, should flash for a few different notifications on your Atrix 2 with out any app triggering it.
Green - Emails (Gmail and Other), Messages - text or vm, and missed calls
Red - battery almost dead
Orange - battery low indicator
There are a few apps out there that allow you to customize the LED color to your liking. Handsent (text messaging app) allows you to change to color for texts only.