Heavy items, such as chocolate chips, tend to sink in cakes, quick breads and muffins as the lighter batter bakes and rises around them. The chips also release oil as they melt, which also helps them to sink. Reserve 1 to 2 tablespoons of the flour called for in the recipe and use it to dust the chips. Fold the floured chips into your batter just before pouring it into the baking pan for baking. The flour helps absorb some of the oil and moisture of the chips so they stay in place.
Another way to prevent major chip sink-age is to use smaller chips. Switch from standard chips or chunks to mini versions, which are lighter and less likely to plunge. If you don't have minis on hand, chop standard chips into smaller pieces.
You might also opt to not stir the chips into the batter at all. Instead, sprinkle them over the top just before you put muffins or cupcakes in the oven. If you've made a full-sized cake or quick bread, cover the bottom of the pan with one-half of the batter and then sprinkle half of the chips on top. Top with the remaining batter and sprinkle the rest of the chips on top. This way, when the chips do sink, they have farther to go and probably won't reach the bottom.