if i make a custom mouse with a sprite on
Ambiguous! Do you mean you added a Sprite-node to the scene and let it follow the mouse cursor? Or are you talking about actually changing the mouse cursor?
hover it over an Area2D(with body enterred signal)connected to the canvaslayer.
You keep mentioning the term "CanvasLayer". Are you talking about the default CanvasLayer which forms the root-node of the scene-tree or have you actually added additional ones to the tree? Also: How is that relevant here?
The Area2D will actually not detect it
Why should it? A Sprite-node is not a body, thus no body is entering the area. The
body_entered-signal will only trigger on a Kinematic-, Static- or RigidBody.
I still don't get what's your problem and where you need help...