To direct maniulate a knot, click down in the view window near the bead you want to move and drag in the direction you want it moved. It helps to be in Beads and Sticks mode. You can also rotate the scene as usual with the left mouse and scale with the middle mouse (but you can't translate). Beads are always moved in a direction perpendicular to the line of sight.
Note that you can display the knot energy while you're manipulating the beads.