Ideally, the screen layout of any application should reflect the way you use it. The functionalities which you use the most should get the lion's share of screen space; less-used functions should be tucked away or hidden so they don't distract you. You can customize the Take Command interface by moving and resizing components, detaching and docking them, or hiding and revealing them.
To move the Folders, List View, and Command Input panes, simply grab the desired pane's title bar and drag it into position with the mouse. As you drag it, notice the little blue graphical ‘targets’ which appear and disappear as you move the mouse over the main Take Command window. Dropping the pane you are dragging onto one of those will re-dock it. (If you don't see the targets, you need to change the pane's display mode to “Dockable” — see below for details.)
The targets at the outer edges of the window attach the pane you are moving to the outer edge of the main Take Command window (and therefore make the pane the same width or height as the Take Command window.) The targets which appear within the other panes allow you to dock the pane you're moving relative to the second pane (and therefore make it the same width or height as that one.)
The Folders, List View, and Command Input panes (but not the tabbed console pane) also show a “tabbed” docking target in the center, allowing you to drop one pane on top of another. If you stack two panes this way, Take Command will display little tabs which you can use to bring either one to the front, or to drag one off the other.
Docking targets allow you to attach one pane to another.
If you drop a pane anywhere other than on a docking target, the pane will become a free-floating window which you can move and resize like any other application window. To re-dock it, simply drag it again and drop it onto a target.
The tabbed console pane cannot be moved by dragging its title bar. To move the console pane relative to the other panes, move the others. For example, if you want the console pane to be to the left of the Folders pane, just drag Folders to the right of the console pane.
Individual panes can be resized by dragging their borders. The main Take Command window can also be resized by dragging its outer edges.
The Folders, List View, and Command Input panes each have a pair of icons which allow you to control their display modes. The first icon, usually a triangle pointing down, allows you to switch a pane between dockable, floating, auto-hide, or hidden modes. Dockable is the default state. In floating mode, a pane is detached from the main Take Command window and can be freely dragged anywhere on the screen; the docking targets will not appear when a floating-mode window is dragged. In auto-hide mode, the pane slides out of view when it is not selected; a small tab remains, allowing you to reopen the pane when you want it. In hidden mode, the pane is not displayed at all; you can reveal it by selecting the appropriate item in the View menu. (Note that the Folders and List View pane are hidden as a pair; you can't hide just one of them.) The second icon, which usually appears as a pushpin, toggles auto-hide mode on or off.
The various toolbars and menu bars can also be moved around, detached, or docked. To drag a toolbar or menu bar, grab it at the end marked with a ridge or a row of dimples (depending on your current theme.) You can hide and restore toolbars through the View / Toolbars and Menus menu.
All of this is far easier to do than it is to describe or read about. Play with the interface! Grab a pane or a toolbar and drag it around the screen. You'll get the hang of it quickly.