Does your son have a 504 plan? If not, I would get him one ASAP. CCFA has a great template:
http://www.crohnscolitisfoundation.org/resources/template-section-504-plan.html
Here is info on 504 plans:
http://www.crohnscolitisfoundation.org/assets/pdfs/504factsheet0816.pdf
The school is required by law to accommodate him. Things like access to the bathroom -no questions asked, stop the clock testing, extensions for assignments if necessary, not being penalized for absences, two sets of books, being allowed to carry a water bottle at all times - things like that are listed in a 504 plan. There may more or fewer accommodations, based on his condition.
If he is really sick and unable to go to school at all, then they may decide to put him on hospital/homebound schooling for a while. A tutor would come to your house for a couple hours a week to catch him up on school work. We have done that in the past. Obviously, it's used as a last resort - being in school is preferable, for both the kiddo and the school! But it is an option for a child who is very sick and unable to get to school.
We do give probiotics with antibiotics. We use Culturelle. Some parents use VSL#3 which is a prescription strength probiotic.
I'm going to tag other parents with teenagers:
my little penguin
pdx
Tesscorm
Clash
Mehita
Jmrogers4
What medications is your son currently on?
Typically, doctors will start with either steroids or exclusive enteral nutrition (a formula only diet - no food, only shakes) to induce remission. A maintenance medication is started at the same time, since they all take a while to work. Usually an immunomodulator like 6MP or Methotrexate or a biologic like Humira or Remicade, or some combination of them.
It does take a while for kids to start feeling better - hang in there!