Omega 3 oils are great for reducing inflammation and shouldn't interfere with your meds.
Fairly high doses are needed to treat an IBD flare. Patients with ulcerative colitis have abnormally low blood levels of EPA. Clinical trials have shown that supplementation with fish oil (2.7 grams of EPA and 1.8 grams of DHA daily) can reduce the severity of the condition by more than 50% and enable many patients to discontinue anti-inflammatory medication and steroids. I believe I've seen dosage recommendations up to 5 grams/day.
Check out the book The New Eating Right for a Bad Gut which contains detailed info about omega 3 supplementation.