Whether or not to amnio is a tough decision, and while it's hard to know the "right" thing to do, getting as much info as possible will at least help make your choice an educated one. In other words… good question.
You'll go in for the amnio somewhere between weeks 15 and 20. First, your doctor will do an ultrasound to locate a pocket of amniotic fluid a safe distance away from both baby and the placenta, which can take up to 20 minutes. Your belly will be cleaned with iodine or alcohol, and your doctor will then guide a long, thin hollow needle into your stomach, through the abdominal wall and into the fluid sac. About an ounce of amniotic fluid (roughly two tablespoons) will be drawn into the needle, which can take from 30 seconds to a few minutes. (Don't worry, baby will produce more to make up for what's taken.) It may seem scary to have a needle so close to baby, but with ultrasound guiding the entire procedure direct injury is very rare. (On the off chance baby does brush against the needle, he'll simply move away quickly — same thing you'd do after hitting something sharp.) Once enough fluid is obtained, the needle will be removed, and you're all done! Your doc might check baby's heart rate with an external fetal monitor to make sure he's doing okay. If your blood is Rh negative, you'll receive a shot of immunoglobulin after (unless baby's father is also negative), in case your blood mixed with baby's potentially non-compatible blood during the test.
The extracted amniotic fluid will be sent to a lab, where baby's cells are taken from the fluid, grown in a culture for about 10 days, and then studied for chromosomal abnormalities. The cells can also be tested for any genetic disorders you may be at risk for. And, the alpha-feto protein levels in the amniotic fluid will be measured, which is helpful in detecting neural tube defects. Structural defects like a cleft palate can't be detected with this procedure, but if you're interested, baby's gender can. You should get the results back in about two weeks.
For you, the procedure might be somewhat uncomfortable, though some women don't feel a thing – pain levels vary greatly between women, and even between pregnancies. It'll probably feel like cramping, pinching or pressure. You may be offered a local anesthetic first to numb the site, but the anesthesia injection might actually be worse than the amnio itself! Make sure someone is available to drive you home afterwards, because you'll need to take it easy for the rest of the day, and avoid sex, heavy lifting and flying for the next three days. You might experience minor cramping, but if they become severe, notice leaking amniotic fluid or spotting, or develop a fever (possible sign of an infection), call your doctor right away — these are all signs of potential miscarriage.
American College of Obstetrics and Gynecologists. Your Pregnancy and Birth. 4th ed. Washington, DC: ACOG; 2005.