There are several keyboard shortcuts that alter what left-clicking on a player or dragging a waypoint in the play designer or formation designer does.
Right-Click
Right-clicking on the field, on a player, or on a waypoint will bring up a context menu appropriate to the shape that was right-clicked on.
Left-Click
Left-clicking on a player will make that player the primary target and highlight him yellow to indicate this. Left-click on the primary target again to deselect him.
CTRL-Left-Click
Holding down the CTRL key and left-clicking on a player will make that player a secondary target and highlight him orange to indicate this. CTRL-left-click on a secondary target to deselect him or left click on the field to deselect all secondary targets.
Left-Click on the Field, Hold, and Drag
Left-clicking on the field, holding the mouse button down, and dragging the mouse will show a box that allows you to select multiple player targets at once for positioning.
Left-Click on a Player or Waypoint, Hold, and Drag
Left-clicking on a player or waypoint, holding the mouse button down, and dragging the mouse will move the player or waypoint.
SHIFT-Left-Click on a Waypoint, Hold, and Drag
Holding down the SHIFT key when moving a waypoint will restrict where the waypoint can be moved to a set of sixteen specific angles around the previous waypoint. This allows you to align waypoints with each other more easily than trying to do so using the free-form drag and drop.
CTRL-Left-Click on a Player or Waypoint, Hold, and Drag
Holding down the CTRL key when moving a player or waypoint will move the player/waypoint and all waypoints after it. This allows you to reposition a player while retaining his route or reposition a waypoint while retaining its relation to the waypoints that follow it.