Kidney stones are not necessarily going to cause you any pain while in the kidney; unless they become infected. The pain comes when the stone tries to pass through the ureter into the bladder. Think of it like a basketball caught up in the branches of a small tree. While the ball is sitting up in the branches, its not causing any disruption. However, if that basketball falls out , and goes into that tree trunk(that is thinner than the ball), its going to become difficult to get that ball all the way down the trunk. Same thing with a stone.
Now, with all that being said, your stones are WAY too big to even try to pass through the ureter. They will probably just sit in your kidney and get bigger, and most likely become infected at some point. Your Dr. is right; you need to have them removed (usually by a procedure called lithotripsy), before they cause any problems in the kidney.
Ive probably had 14 lithotripsy procedures. They're not fun, but they are not horrible. Its done on an outpatient basis. You will go in and they will pulverise the stones with some type of sonar waves. The stones then become sand, and can easily pass through the ureter.