Dogs don't generealize. They think commands are only obeyed the way they were taught. Its up to you to train them that a command is a command regardless where you are or what you're doing.

You trained them standing up, most likely standing right in front of them. They learned that commands are obeyed when standing. They never had to obey a command while you were sitting. You need to start on simple commands while sitting (like "sit") if he doesn't sit, say a sharp sound to get his attention and motion for sit along with the verbal command. Offer treats and praise for doing it while seated. Repeat, repeat, repeat.

Many people fail to realize just how imporant this is