I have also encountered difficulties arranging the SCID windows in various configurations such as what you are describing. I don't have a solution to your question but I would sure like to hear it if someone knows how.
Just in case you don't know; if you have a config which you like, you can save it under {Options/Windows/Save Layout/] where SCID provides three save/restore choices.
On the Scid webpage, there's a screenshots link. It shows various examples where the different scid windows have been placed in different locations. For example, "variations" has the engine analysis below the game board. I cannot figure out how to do this. You can right click and get "move to bottom, etc", but this doesn't get me there. Also, I can "undock" but can't see how to redock.