Is either the sphere, the dimple a component or group? In order to get the dimple into the sphere, all of the geometry needs to be in the same context. That is, either none of it grouped or all of it in the same group. If you can upload your model as you’ve got it, it’ll be easier to help you sort it out.
In general, when I need to do something like this, I would make a component of the sphere, draw the dimple and move it where I need it to be on the sphere. Since the dimple geometry would be outside of the sphere component, the dimple can’t modify the sphere. When I’m ready to modify the sphere, I would select the dimple geometry and cut it to the clipboard. Then I would open the sphere component for editing and use Paste in place to put the dimple geometry in place. Select all of the geometry, right click and choose Intersect Faces>With Selection and erase the unneeded geometry.
I used keyboard shortcuts some of the operations.
Select the sphere for the dimple.
Cut to clipboard.
Open sphere component for editing.
Paste in place.
Intersect Faces>With Selection.
Select the unneeded part of the dimple sphere and delete it.
Select the skin over the dimple and delete it.
Correct the reversed faces in the dimple.