Yes, there are differences. It depends on the type of coral, for example, in the polyps of some species of Zoanthus a higher concentration of zooxanthellae is found in the tentacles of the polyps. It depends if the polyps are in the center or at the edge of the colony.
Zooxanthellae densities in coral colonies are very closely linked to areas of calcification. Here are a couple of links to papers that you may find interesting: