Bubbles shouldn't settle really as gas is generally lighter than water. Are you sure they aren't eggs? What fish have you got in your tank? Can you snap a picture of the "bubbles"?
might just be trapped air. If you gently disturb the surface of the sand with a stick (I've read of people using a chopstick to great effect) it should release the trapped air Nothing to worry about really.
With sand though, you want to make sure you have fish that will keep the surface turned over. Sand that is left alone can compact down and toxic gas can start to form. Now, some say its not enough gas to cause a problem, some say it is. I've not had experience of it so can't really say. Basically I think some bottom feeders that like to rummage in the sand are always a good thing (think cories etc).