Click on the spotter or hq unit, the arty panel opens, clck on flares (the left most icon), right click on area to illuminate and you should see the tooltip for the flares button chage to time to fire. Remember to click on the button again to tell the arty unit to stop illumination otherwise they will fire off all the flares. Artillery/airstrike works in the same way but you right click and drag to specify the area you want targeted.
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