i learned as a wee cyclist that the ball of your foot should be directly above the pedal spindle. if this is where your foot is with clips, you may simply be adjusting to "correct" foot positioning. it all depends on how you were riding without clips. I seem to recall that learning to use clips was a process of getting used to having my foot a bit farther back on the pedal. Without clips, one is prone to mashing down with the middle of the foot, or at least the flat of the foot just aft of the ball, for maximum stability/pressure. With clips, one has the advantage of the clips for stability, as well as the additional power of the upstroke, which negates the need for such uncivilized mashing.

however, it sounds like your clips are too small.