You will have to target them individually in order to save the girl and then suck them into your gun to get bonus at end of each level. (gearnuke.com)
If they are switched one way they will be pulled towards each other, whilst they can also be switched so that they push each other to opposite ends of the level. (gamegrin.com)
If you wanted to implement say a bonus room you could just leave space at the start / end of a level blocked off by a wall. (reddit.com)