Both my girls have been on Remicade and Methotrexate. My younger one had a hard time with MTX - severe nausea, some vomiting and dizziness. No side effects at all with the Remicade. We tried every tip in the book so that we could keep her on MTX, since it worked so well for her joints and gut, but eventually she just refused to take it anymore.
Her reaction was kind of extreme - MOST kids have no side effects or very mild, manageable side effects.
Anyway, 8 months after starting the Remicade + MTX combination, my younger daughter was scoped again. Her colon looked "beautiful!" All the ulcers and inflammation they had found during her first scope were gone. Biopsies were clean in her colon, and showed only mild inflammation in her TI. It was really incredible.
My older daughter is still on Methotrexate but now on Humira instead of Remicade. She also did very well on the Remi +MTX combination. She had some nausea with MTX, but it was easily taken care of by Zofran. She is doing great!
I was worried about adding MTX to their biologics - it sounded like such a scary drug. In fact, it even kept me up at night for a while! But after a while, the drugs start to seem less scary than the disease, and we've never regretted adding MTX - not even for a second.
This is a good presentation on the risks and benefits of IBD drugs:
http://programs.rmei.com/CCFA139VL/
Good luck!