I think many teens find talking about their bathroom habits embarrassing, so be forewarned about that and encourage him to be open and informative. GI's hear this stuff all day long and nothing will surprise them. The doctor is going to ask a lot of questions. Maybe discuss with him beforehand whether he wants you in the room as well - don't assume he does or that you're allowed to be there. Are you his legal guardian?
There will likely be a physical exam. Look in the mouth, feel the stomach, possibly check out his bottom. Depending on his symptoms, maybe even an anal exam. Also a blood draw for labs. If the timing works out, maybe even a stool sample. I don't remember if you said he's had scopes done yet, but if not, they may schedule him for a colonoscopy, endoscopy or even an MRE.
Then you wait. At our GI office, lab results are usually back the same day, but I know the turnover isn't always that quick everywhere.
And like Patricia said, start logging everything now. It might get annoying after awhile, but if you go in with everything documented and can say on average he poops x many times a day, has blood x times a week, eats x calories a day... I think you'll be taken pretty seriously.
When you leave ask for copies of everything and be sure you understand what the plan will be.
Hope that helps!