Determining which ToolWindowContainers are on the "left" or "right", really depends on how you are populating the DockSite. You could have several ToolWindowContainers that are located to the left of the Workspace, but are docked side-by-side. The ControlSize can only be set before the ToolWindowContainer is loaded, so you'd typically set this in you XAML or on the ToolWindowContainer after you create it in code-behind.
You can use the SplitContainer.ResizeSlots method to dynamically resize items during runtime. We have TODO items marked down to added better support for specifying sizing the windows.
If a ToolWindowContainer is docked to the left/right then you can specify the size as "<DesiredWidth>,200", and it will ignore the 200 until it's docked on the bottom/top. There isn't currently a way to set only the width or height, but you could get the current ControlSize, change just the width, then set the ControlSize.