Inside the tank itself when the bubbling happens the bubbling is coming from a black tube on the left of the tank that one side is screwed or glued to the tank which is under the toilet on top of the tube is a circular yellow vented thing on one side is a rod that the black ball is on. Well when the bubbles are done and I flush then it moves to the other toilet on the other side of the house

Take a look at this fill valve diagram. Try explaining your issue using theses labels. http://411plumb.com/wp-content/uploads/2009/08/fluidmaster-400a-diagram.jpg