I picked up running last year. I had to take this year off due to a pilonidal sinus issue, but I have discovered a few things (with the help of a running coach for the Crohn's and Colitis Foundation of America)
1) Hydration is more important for people with Crohn's. For whatever reason, even in remission, people with Crohn's go through more water. Run with water.
2) Salt helps calm the belly. I like the gatorade and CLIFF branded ones. Check the sodium content. The Cliff margarita contain the most electrolytes for Cliff. I keep a few blocks in my pocket and pop them if I start getting crampy.
3) Post run fueling - Make sure you eat enough protein. Boost is a great brand of nutritional shake that has been studied to absorb easy even in a flare.
4) Sometimes it sucks - Even in remission for 15 years, there are days where you're just going to be miserable. You have to learn when to bail and when to push through. For me it got better over time.
5) Diet - Pay very close attention to you pre-race food. I found I would eat complex carbs prior to racing an it helped some
6) Be aware that people with Crohn's can have blood sugar issues. I use the gels as my primary fuel source. For long runs, I'll sprinkle a tiny bit of gatorade powder into my water. I do water for bottle 1 and gatorade/water for bottle 2