It's not always easy. An accurate diagnosis can be difficult because of the way movement disorders can resemble one another. The docs will try and make a diagnosis based on the exact nature of your symptoms as well as your health history.
For dystonia, they can do a test called an EMG, where they insert sensors into the muscles that are misbehaving. If it's dystonia, the test will show specific electrical pulses being sent to the muscles, even when they aren't in motion. In addition, dystonia tends to get worse if the person is fatigued, stressed, or cold -- so the doc would ask questions to see if this is the case with you.
For MS, there are some basic tests a neurologist can do in the office evaluating reflex reactions (like when they tap your shin with a mallet, or scrape the bottom of your foot). If the neurologist suspects MS, then an MRI is the next step. There are certain kinds of lesions associated with MS that an MRI will pick-up. The MRI is considered a very reliable to way to confirm a MS diagnosis.
As for eye twitching -- yes that can have many causes, everything from stress, to seizures, to medication side effects. In the case of a seizure, the eye twitching tends to occur as part of several symptoms rather than on it's own. As with other neurological disorders, the neurologist will look at symptoms in the greater context to try and make a diagnosis.