Here’s how I’d do it:
1. Clone both objects onto whatever you’re cloning onto;
2. With the cloner selected, use the Mograph>Mograph Selection tool to select the spots where you would like a particular clone to be placed;
3. Create a Plane Effector, which will automatically be restricted to the Mograph selection you just created;
4. Turn off the effector’s default Position parameter and set the Parameter>Modify Clone slider up to 100%.
That will place only the second object under the cloner on your selection set.