I used Soy Iso's this cycle on CD's 2-6. I am now on CD 8 and just waiting for ovulation.
I took 80mg, 80mg, 120, 120, 160... I researched it alot and from what I understand, taking it for just the 5 days will not negatively affect fertility but you have to be careful to avoid all soy for the rest of your cycle. Too much soy can mess you up even more which is why I started out with the lower doses instead of jumping into taking 200mg a day like I have seen some women do.
It's also my understanding that you should not use them if you have a regular cycle and you ovulate on your own, although I have read some contradicting things about that saying that even if you do O on your own, that soy iso's can give you a stronger ovulation and a bigger/more mature egg.
For me, I chose to try them out this month because we have been TTC for almost a year now. I was on the depo shot for 9 months and it took my AF 9 months to return and since then my cycles have just been all over the place.. one month it will be 40 days, the next it will be 18 days... My most recent cycle was 27 days which was the closest to normal that I've had so far but I decided to go ahead and try the soy this month after reading several success stories.