Three days is actually normal for some (healthy) people to go without going, so I don't think it's something your bowel can't handle. And if you then went four times, it doesn't sound like you could have a blockage now.
However, amitriptyline can be extremely constipating. If you go several days without a bowel movement, or it is extremely hard and requires a lot of time and/or straining to get it out, you may need to counter it with a stool softener or laxative. This is what I used to do to counter the effects of ami - and I was usually so diarrhoea-prone! The ami was far more constipating than anti-diarrhoea meds like loperamide and lomotil. Now I have an ileostomy so I can take all the ami I want without a problem.
Dose plays a role usually too - reducing the ami may reduce the constipation, but may reduce it's beneficial effects as well. I'm on a high dose of ami but have tried different doses and there is definitely sometimes a correlation between dose and severity of side effects, yet other times I get side effects regardless. I've also found that some side effects eased or disappeared over time - after several weeks of taking ami. Yet, again, other effects are just as strong now as when I started taking it over a year ago. It's just a really tricky, unpredictable med. It can do an awful lot of good, but it has a lot of side effects to manage. Don't give up - stick with it, adjust the dosage, try to counter the side effects. In this case I'd start with stool softeners, as they are usually much more gentle than laxatives, and you don't want to go too much in the other direction, especially having IBD.
Have you discussed this with the doctor who's prescribing it to you? What is been his/her opinion?