When you are breeding eggs, you can bring the pokemon you wish to raise happiness with you and equip a soothe bell (obtained in Shalour City) on it. Activate the Befriending O-power while you are walking/riding bicycle, keep re-activating it once it goes off. After about 2 rounds of eggs you may obtain a pokemon with a high happiness level
P.S. Also you can go to Cyllage City for a pokemon massage, but I personally think that the effect isn't very significant. You can check the level of happiness of your pokemon in Laverre City.