For me, it would be by context. If you said 'my stomach hurts' than i know it's the inside. If you say 'there's a mark on my stomach' it has to be the outside. I can't think of an example that could be used for both...

The word 'stomach' is sometimes used in a third way - "I can't stomach going into work today" or "I wish I had the stomach to do that". This is slang and not encouraged but you might come across its use. Its basic use here is to say that "I can't face (don't want to) going into work today" or "I'm not brave enough to do that".

(I'm a US native speaker). We distinguish by context. There is a great deal of overlap in the meanings of words related to this part of the body. I would be more likely to say "belly" than "stomach" if I meant the external abdomen. There is a similar ambiguity between "gut" and "belly." Normally, the "gut" is the intestine, but it, too, can mean belly. For example, in "Stand up straight and suck in your gut!" the last phrase means "tense your muscles so as to flatten your belly." Similarly, we might say "he was overweight, with his gut sticking out over his belt." "Guts" means all of the viscera. "A stomach-ache" means any abdominal discomfort, not necessarily in the stomach. And, of course, especially when talking to children, "tummy" means the whole abdominal area--it's a childish mispronunciation of "stomach."