I think you're getting the concept of a "ceiling" confused with cloud clearance regulations. They're two different things.
A "ceiling" is a layer of clouds that is greater than a certain density. YouAt least in Class D airspace, you can't fly VFR at all unless either there is no ceiling, or the ceiling is more than 1,000 feet above the ground.
If it is legal to fly VFR, then you still have to stay a certain minimum distance from any clouds, regardless of if any given cloud is part of a layer or not. So, a single cloud in an otherwise clear sky wouldn't constitute a layer, much less a ceiling, but you do still have to stay away from it.
The phrase "1000 feet above" means you are the one that's above the cloud, not the other way around.