The bubbles that your referring too is a healthy sand bed. Its normal to see tons of lil bubbles under your sandbed. I believe its air that has been trapped and turned into nitrogen. Don't stir it your sand bed all up at once since the nitrogen bubbles can have a bad effect to your tank, its best to let a sand sifter do it slowly if you don't like seeing it.
Their is nothing wrong with having them remain under your sand. I don't have any sand sifters in my tank.