I'm in a slightly different situation. My son has a genetic disorder which is actually fairly common (about 1 in 120 boys will be affected). At my first appointment with the real OB, he said, "Because you have a child with a genetic disorder, we're obligated to offer you genetic testing; these are the things that we can do." I nearly fell over laughing, because my son's disorder really isn't a big deal. It's only life threatening under particular circumstances which are, in the modern world, *very* easily avoided. Plus, because my husband is unaffected and this is a sex-linked trait, the child I'm carrying would have to be a boy and would still only have a 50% chance of being affected. In my particular case, amniocentesis just struck me as an unnecessary risk; far easier simply to avoid the potential dangers to my potential son, you know? Knowing would change nothing about my prenatal care, nor about his care immediately after birth.
So we'll wait until the newborn screening to find out about that.
The issue which concerned me more, however, was the congenital condition which my daughter has. Due to that, and the misery it put me through, I will have a level II ultrasound in about a month and a half. The risk of having a second child with this disorder (or another kidney disorder) is quite low, but it's about 30 times the risk for someone who *doesn't* have a child/first degree family member with it, and I'm the sort of person who needs the most information possible. The kidney issue could potentially change the baby's care, post-birth, and that's noteworthy.
In your situation, I'd ask myself the following questions:
1) What do I know so far, for certain?
2) What will I learn from further testing?
3) Is there anything that I could learn which might change:
a) The prenatal care I'm receiving?
b) The way the baby is cared for after birth?
c) The outcome of the pregnancy?
4) If I did learn such a thing, what decisions would I be likely to face?
5) What would I do, in event X?
My personal inclination is toward the least amount of testing for the most amount of result. Amniocentesis is a serious procedure; you're talking about physically invading your womb and the amniotic sack and withdrawing fluid. While most of the time this goes off without a hitch, there are risks involved for both you and the baby. Any doctor who does not inform you of these risks is not doing their job. For something like my son's genetic disorder, I just don't see a procedure like amniocentesis being a reasonable option; knowing in advance whether or not the child is an affected boy or a carrier girl (and of course my girls have a 50% chance of being carriers) is not going to change anything in any meaningful way. In my case, the risks of amnio are totally unreasonable to take. If, however, I was at high risk for another disorder which could significantly impact life for me, the child, both of us or our family then I'd have to consider it much more thoroughly.
If my BooBah's congenital anomaly was readily detectible through amnio, I would probably want it done-- *after* the ultrasound (again, the less invasive procedure).
Best of luck in making this difficult decision.