ediff-control-frame-position-function is a variable defined in `ediff-wind.el'.
Its value is

  • This variable may be risky if used as a file-local variable.

Function to call to determine the desired location for the control panel.
Expects three parameters: the control buffer, the desired width and height
of the control frame. It returns an association list
of the form ((top . ) (left . ))

You can customize this variable.