Sorry you are going through this now. I know in the past there have been posts about not saying too much when you first apply for a job. However, now you are into a flare and need the time. First, I would definitely get a doctor's note. Second, I think it is time to explain UC to your boss (and HR and anyone else who needs to know).
I know my daughter is still young and only has a part-time job but she started in August 2006 and was first hit with UC in September 2006. Because it was so new, she would call and say she wouldn't be in for the week (10 hours at the time) but would probably be better by the following week. Well one week turned into 2 which turned into 3, etc. until it was 9 weeks later. She is on her 3rd flare and still has her job (albeit it isn't a tremendous problem for them if she isn't there). Once we understood UC, we have been very open and upfront about it to her job. Exactly what it is, what happens, etc. The funniest thing to me is that they always ask questions about it and she works in a library! I always want to say...LOOK IT UP!