I made a bunch of shapes and joined them and now want to take those shapes, copy them, and place them on top of the original shapes to use the punch out option. I can create a clone of those shapes via the clone command or I can just drag the layer down to the new layer icon to copy them that way. Just wondering if there is a reason/benefit to doing this one way or the other in the long run?
When you clone a collection of objects, each clone appears above its original source object—like layers in a sandwich, the original and the cloned objects are interspersed with one another. Whereas if you drag a layer to the new layer icon, the copy will be self-contained (like a second sandwich!).
Other than this difference, there's no reason to use one or the other. If you use the Combine Paths commands on objects across multiple layers, the resulting object will wind up in the bottom-most layer, I believe. You may wind up with an empty Layer folder that you'll want to delete.