The 'positions' are high hang, hang/above knee, below knee, midshin/floor. Obviously that's four, so its up to you which you use. Two position clean means one rep = two cleans, each from a different starting position. For example, a clean from the high hang, then keeping the bar in hand, a clean from below the knee.
Traditionally if you want to work on technique, start high and go lower; if you want to work on improving power (on the background of sound technique) then start low and go higher.