Well the first thing to do is NOT muscle through the pain. If you start feeling pain, stop before you make it worse. How do you hold the guitar when you sit down; resting on your left or right leg? If you rest it on your right, standing up will be way different since the neck is further away from you and you have to bend your wrist more. It just takes some getting used to. There is no one right place to have your thumb, its just what feels comfortable to you. Generally you either want to have it in the middle of the neck or higher. If you have longer fingers, go higher on the neck, but if you have shorter fingers, you may not have the reach.

The lower your thumb goes, the more you have to bend your wrist, and the more stain you put on those thumb/palm muscles. I've noticed this problem too, and for me its the fact that I have shorter fingers, so I really have to bend my wrist to play.