Working with/without the manipulator in Silo.
Silo is a manipulator-based program, though you can now use it equally well with the main manipulator turned off if you prefer.  The main manipulator centers itself on your selection, while the alternate manipulator stays in the corner of the screen.  Either can be clicked on and dragged to transform your selection.
There are five different options for your manipulator tool: universal, move, scale, rotate, and no manipulator.  These are accesible from the right-click menu or from hotkeys "Q", "W", "E", "R", and "T".


Each of the manipulators has handles that you can click and drag on to perform their respective operations in the axis chosen.  For example, click on the green arrow of the move manipulator to move your selection in the direction it points.


You can also use keyboard shortcuts to constrain your operation to a particular axis or plane.  If the move manipulator is the active manipulator and you press a keyboard shortcut assigned to "Constrain to XZ Plane", moving your mouse will move your selection in the plane of the manipulator's x and y axes.  Alternately, if you click and drag on the manipulator's z axis, then press a key to constrain movement to the x axis, motion will also be constrained to the xz plane.
You can adjust the manipulator's orientation from the Orient Manipulator and Auto Orient Manipulator sub-menus in the Selection menu.  The Auto Orient menu will determine how the manipulator is oriented at each new selection, while the Oreint menu will perform the orientation only for the current selection.  The Enable Repositioning check allows you to set whether the manipulator repositions (as opposed to reorienting) itself when a new selection is made.


You can toggle the display of the manipulators in the Display menu (Display > Show Manipulator and Display > Show Alternate Manipulator).  If you want to work without the manipulator, we suggest you turn off the display of the main manipulator and leave the alternate manipulator on, so you can tell which manipulator tool is active.


If you want to move or rotate the manipulator without moving or rotating the selection, activate manipulator edit mode (Selection > Manipulator Edit Mode or press the Insert key).  The manipulator will turn all white to signify that you are in this mode.  Uncheck the menu item or press Insert again to exit the mode when you have positioned and oriented the manipulator how you want it.