It always annoyed me in the Oblivion CS how the three primary windows are separate windows floating inside the overall CS one. I was hoping that would go away with the Skyrim version, but no such luck. Is there at least a way now to dock the windows into a permanent position, or snap them into a certain configuration on opening? Every time I open the CS I have to re-arrange the Object, Cell, and Render windows how I want again.

No, the CK does support any docking/snapping facilities.

I find that if I size the three windows so that they don't overlap, or obscure the main toolbars / message footer, the toolset always reopens in much the same configuration.

Sometimes one of the windows seems to slip down the screen a tad, but correcting that is trivial.

I have all three windows overlapping each other. The render window and the cell view window overlap by 80%. They load to that same configuration every time I start the CK. On occasion, the object window does not appear after loading, but just clicking on either the render or the cell view window brings it up.

I'm not sure but think you have to take ownership of the Skyrim game folder (Windows7 x64) . It seems like the CK cannot write to SkyrimEditor.ini and therefore can't save your setting.
I tried to change some settings in the SkyrimEditor.ini file and the computer refused to save the changes. The only way was to take ownership of the folder and set the permissions manually.

Bummer.
My local Administrators group was the owner and that includes my account, but I switched Owner to my account anyway and rebooted, but the windows are still all wacky when I start the CK back up. Guess I'll just have to live with it for now.

Thanks for trying guys! appreciate it