Upon further reflection, call the prescribing doctor (doc that prescribed the Topamax) and let him/her know that your son has these symptoms.
I'd do it right now, just to be on the safe side.
And I meant topAmax with an "A", not an "O"... sorry for the misspelling.
Topomax has some common & uncommon side effects, and stomach pain & back pain fall into the uncommon, but the burning urination is a little concerning.
What leads you to believe it could be appendicitis, and not something like a UTI, or bladder infection? Just curious.
I'm not a doctor, just letting you know, but I have a little experience with Topomax (never experienced those particular side-effects myself mind you).