Polycystic ovaries is caused by immature eggs, which do not grow and release into your fallopian tube, but instead clusters around the ovary, causing decreased ovulation. It does affect fertility in as much as if you are not ovulating often or at all (because a mature egg is not being released) then you can't get pg. However there are various ways of trying to overcome it and they can be successful.
The first step will be to check if you are ovulating and to get you doing so regularly. This is usually done by taking certain hormone related pills, probably something like Clomid. This is tried for a few months starting at one dose and maybe increasing it if ovulation does not occur.
If Clomid is unsuccessful there are still other options to be considered. Ovarian diathermy can be performed, which isn't as scary as it sounds! It basically involves removing tiny amounts of ovary using a laser through a laparoscopy (goes in through your belly button). For reasons that noone seems to know this often does the trick and gets ovulation established again.
I know all this because it is the course of events that unfolded to me. I was trying for my second child like you when I discovered i had polycystic ovaries. Clomid didn't work for me, but after having the diathermy done in the february I was pregnant in the following April, and now I have 4 children! Obviously did their job too well!
The only other thing I can add is that I was told to complete my family within about 3 years as the effects of the op tend to wear off by then, although I had this done in 1996 and had my last child last year, so it lasted longer for me.
I really hope this helps you. Good luck!