Biome mods like Biomes O' Plenty and Biomes XL are automatically supported by Chocolate Quest. You don't have to do anything to make dungeons spawn in biomes added by those mods.
Chocolate Quest checks to see if there is a good spot for a dungeon before it spawns. Many areas are too mountainous for dungeons to spawn. If you would like to see dungeons appear more regularly open all of the .prop files in your .minecraft\config\Chocolate\DungeonConfig folder and change chance = X to a lower number. For more information on editing the config files read this article.