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"on top" and "over" could mean the y or z ordering depending on the context, and you were never specific.
Look at the glass pane and the layered pane

I do not understand the effect you are trying to achieve, perhaps a screenshot of what you want, or some code to show what you are attempting to accomplish?

What do you mean by "over every other element"?
---What ever, the answer will still be 'No'
JFrame is a Container and will function like all other Containers in terms of how things are treated when...

No it is not. A component can only be in one place at any given point in time. If added to a new/different container, it will remove itself from its previous container (as shown by your tests). I do...

See post #5.
Learn to use layout managers, it is not hard, and very helpful when used correctly.

Do not force the size of the frame. Set the preferred size of the JPanel, add everything to the...

The panel is never added to the frame, fix that first...

Sounds like a bug introduced by the the code itself. Post the code in question where we can have a look