Your question is very broad. Nystatin has it's place in fighting Candida, as do a lot of other anti fungal drugs. Depending on which strain of Candida is overgrowing in your body and where the location of your Candida overgrowth is makes all the difference when choosing an anti fungal drug to take. Also, you have to remember that some strains of Candida have become resistant to one anti fungal drug or the other. So while one anti fungal might work for one person, the same drug might not work for the other.
Which area of the body do you feel that you have a Candida overgrowth?
As with any prescription drug (or even some non prescription drugs for that matter), there is always the possibility of side effects. You as a patient must assess your situation, and then determine if taking the drug or supplement is appropriate.
When I had my tonsils removed, my doctor prescribed me a prescription strength pain reliever afterwards to help with the pain (I can't remember if it was Vicodin or Lortab). Anyway, after about 3 days of taking it I started getting really sick (nausea, chills, fever). I called the doctor's office, and they said that was a common side effect from the pain medicine. So they told me they would put me on another pain medicine for the remainder of the treatment. My side effects went away when I was on the new medicine. It just depends on the person taking the medicine and how their body reacts to it.