How do you unclog the bottom drain of a in ground pool if you can't find the junction of the skimmer and the main drain?

Depends how the pool was plummed. If you have a dedicated main drain line, or you share a main drain line and a skimmer line. Both are suction lines to the pump,meaning they will go into the front of the pump. If you have several valves on the front of the pump, and hopefully they are labeled you could try to shut all of them except the main drain and use what is called a drain king. It hooks to a waterhose and swells inside the pipe forcing water in the opposite direction. If you dont have any valves on the front of the pump ,chances are you share suction with the skimmer. check the inside bottom of the skimmer. Main drain may be plummed to skimmer bottom.