You must always* use your smoker to puff smoke into the entrance of the hive before opening the top cover.  This calms the bees while you are working the hive.  Apply several puffs of smoke directly into the entrance, being careful not to burn any bees or tilt the smoker so much that its burning contents fall out.  Wait at least 30 seconds before removing the top cover to allow the smoke to work its way up into the brood box.

Smoking will mask the alarm pheromone secreted by the guard bees waiting at the entrance, so the rest of the colony is not prone to sting.  The smoke also drives the bees to the comb where they engorge on honey, presumably because they believe their tree is burning down, and they'll need to swarm and find a new home.  Of course, you only blow a few puffs of smoke in the entrance, so they stop believing their tree is being consumed by fire.  With the bees full of honey, they will be far less likely to sting.