1st step.....sit on a tall chair or counter and let your lower legs hang naturally. Do your feet point straight or are they angled? You want your feet to replicate that position when you ride the bike so you want to angle your cleats to allow the shoe to do this. You DO NOT want your cleats to force your feet to point in a un-natural position.
The latest thinking concerning where the spindle position is this. The spindle should lie between your 1st and 5th metatarsal. This is normally about 2.5mm behind the ball of your foot. With your foot in your shoe you should be able to squeeze the sides enough to feel where the boney protrusion is that will mark the ball.