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. 

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.

I've made some progress.  First, close all windows except the board window.  Then open up a window you want, like the "Game List".  Right click on that tab.  You now have a "move to bottom" option.  I believe this is the only way you can put any window below the board, which is key.  Most of the layouts I desire have one window below the board.  Now you can open another window, say the "PGN Window".  But !!!!, ....before you do that, click on the Board tab.  After opening "PGN Window", right click on that tab and select "move to right".  If you don't first click on the Board tab, the "PGN Window" will be to the right of the "Game List".  So both the "Game List" and "PGN Window" will be below the board.  Maybe that's what you want.  But if it isn't, and you wanted it to the right (or left or top) of the board, now you know how to get that. 

So I can get just about any window arrangement I want now.  I just have to be very careful to start with only a board showing.  Then select the windows in the proper order and arrange each immediately after opening it.  But it seems you can't rearrange those windows very easily afterwards.  You can save up to 3 layouts with Options-Windows-Save Layout. 

It's too bad that the Windows arrangement capabilities of ChessX aren't in Scid.  ChessX looks like a recent try to build on the Scid platform.  But it's missing most of all the other cool things of Scid.