Seems like I have to write my own window setup function. Does anyone have one they
use? I do want the control panel to share a frame with one of the diff buffers.

What threw me off is that the manual suggests this is possible out of the box, but
I don't see how.

from the ediff manual:
"The files being compared, file-A,
file-B, and file-C (if applicable) are shown in separate windows (side
by side, one above the another, or in separate frames)"
I am using a recent development version of emacs.

- Ian