The lasers are set up in such a way so that on average they kick the atoms in direction opposite of the atomic velocity i.e. cooling them.
That is achieved by setting the laser frequency a little below the frequency at which the atoms will absorb it. That way, only atoms moving AGAINST the laser light will see it dopler shifted to the right higher frequency, absorb it and get a kick in direction opposite of their motion.
In this way, on average, atoms get more absorbtion kicks opposite to their motion. Of course, later they reemit the light by spontaneous emission but the kicks of the spontaneous emission have no preferred direction. The result is on average, atoms are kicked opposite of their motion and slowed down. Since temperature is a measure of the atomic translational kinetic energy, the atomic gas is cooled down.
The most basic set up is two laser beams opposing each other and cooling in two opposite directions and the atomic sample in the middle. More elaborate set up is 3 couples of opposite beams along the X, Y, Z directions.