This is best done right at the beginning of the game since the enemies you'll encounter are very weak.
As soon as you enter combat make sure your teammates draw attention away from you. Circle the enemy group until you are on their side or behind them. The enemy has to take cover while you kill it otherwise it will not count as a flanking kill.
If you wanna make sure it counts just press
while aiming at an alien to enter Battle Focus. If it says Flanked
above the enemies' head...nuke him.