Well, yes, you can watch 3d movie even you have amblyopia. Of course, first you need know something about 3d movie. Generally speaking, when you have worn a pair of 3d glasses while watching 3d movie, it will make you feel that you are just in the real phenomenon. For your situation, you can just have a pair of contact lenses which can do a good job for you when you are watching 3d movie when you have amblyopia. So you can just have a try.
No, people with amblyopia can not see 3D movies. Becasue 3D movies rely on tricking the brain by sending different images to each eye. If you try watching a 3D movie with just one eye closed, the 3D effect will disappear. But people with amblyopia lack depth perception, which is called stereopsis, and this is particularly required for 3D movies and this is the highest form of depth perception, without which 3D movies just do not exist! But if your condition is minimal, then you may get depth perception, but that's really rare. So go to the doctor and have some treatments before you can see a 3D movie.
Normally speaking, I have to say that people with amblyopia can't see 3D movies. There is a condition called stereo-blind, refering to monocular vision, or flat reviewer or lacking depth perception. The most common reasons for the stereo-blindness include vision disorders or loss of one eye's vision. There disorder conditions include amblyopia, squint or optic nerves hypoplasia. In the past, people believe that stereo vision was fully developed and learnt in infancy, for adult people who have stereo-blindness can't get the vision. But according to some reports and researches today, it seems that there is one way out for people with stereo-blind. Recommend one book to you, Fixing My Gaze. Hope it could be helpful. Good luck.