They are mainly on my right ovary and they have disappeared on many occasions. My doctor said that he thinks the cause of my cysts are that I'm producing too much hormones around and after my cycle and as long as I am having pretty regular cycles that he sees nothing to be concerned about.
It's not a 100% hindrance. If only one of your ovaries has cysts, then it may not be much of a problem. If both has cysts, getting pregnant may be harder, so getting rid of the cysts will have to come first. Your Ob-gyne would be the best person to approach for any treatments.
I have cystic ovaries too and I've been on pills and was told to lose weight to get rid of them.