Skyline remembers the layout of the windows in a file whose name ends in ".sky.view" in the same folder the Skyline document (.sky file).
If you find that your window layout is hopelessly messed up, the easiest thing to do is probably to delete the .sky.view file.
You can use the menu item "File > Open containing folder" to bring up Windows Explorer with the .sky file selected.
The .sky.view file is usually the file immediately below that.
If you delete (or rename) that file, and then exit and restart Skyline, when you open the Skyline document the window layout will be Skyline's default.

I am not aware of any documentation about how to drag Skyline windows around and dock them.
The rectangle containing the chromatogram graphs is the "Document Panel". The chromatogram graphs are only allowed to appear in the Document Panel.
All of the other windows are allowed to appear either in the Document Panel, or in a different dock panel.
When you drag a window, Skyline displays up to four drop targets on the four edges of the Document Panel. These are the drop targets which will cause the window to be positioned next to the Document Panel. Those drop targets only appear on the edges of the Document Panel which do not already have a neighbor. (see attached "DocumentPanel.png")

As you are dragging the window, if you bring it over another dock panel, Skyline will display a drop target in the middle of the dock panel with arrows pointing in four directions and a spot in the middle. (see attached "PanelDropTargets.png")

When you release the mouse while dragging a window, the window will be a floating window if the mouse was not pointing at a drop target. If the mouse was pointing at a drop target, the window will be docked based on which target the mouse was over.

I am hoping someone else on this support board can suggest a webinar which talks about this.
-- Nick