I think it depends on how elemental you're going. If you're going to the hospital to start it, I'm assuming you're doing tube and pretty elemental. Most of the more elemental "drinks" aren't very palatable from what I hear. My son did Boost/Ensure for three weeks, but they're much more drinkable. I'm sure someone else with more experience will reply soon. We've never done tube feedings.
Usually, based on what the GI has seen or knows about your son's case, the GI will present you with a couple medication options. Some do the bottom up approach (lesser drugs first, then working up to biologics) and some do the top down approach (start with biologics). It really depends on your GI and where your son is at. Keep in mind that simply being a child with IBD tends to put his disease in a more severe category. Some studies are indicating that top down works best for kids to get the disease under control as quickly and efficiently as possible.
Bottom up:
5-ASA's: Pentasa, Lialda, Asacol, etc.
Immunomodulators: Imuran, Azathioprine, 6MP, Methotrexate
Biologics: Remicade, Humira
Personally, we did the bottom up approach and nothing worked for my son until he got to Remicade. I regret all the time we spent on the other meds (years!) because it was during prime puberty growing time and now he's very small for his age. I see how well Remicade has worked for him and kick myself for not going there sooner. Do your research, but try not to let your fear of the drugs take away from his chance to get better. Ultimately, the decision is always yours, but your doctor has a lot of experience and knowledge too so if s/he suggests something, he's not doing so lightly. The trouble is that IBD is so different for each person, kids even more so, and it's really just trial and error until you find what works for your son.
I think what a lot of parents get stuck on with the medications is worrying about the side effects. MyLittlePenguin has some good stats that she can throw out when she's around next.
Something else to start thinking about (if you're in the US?) is a 504 plan for school. Totally worth the time and effort to get one established.
Keep tossing the questions out...