The three over six rule means that you should see three temps that are higher than the previous six temperatures in order to confirm ovulation.
Here is a link on FF about it.
Fertility Awareness Method
I used to follow this rule strictly and always thought FF was screwy with how they mark their charts. I am starting to get a little more open-minded with ff and kind of like the way they mark their charts now. I have watched a lot of girls on TTC have charts that would have been called annovulatory based on the three over six rule but yet when they had their progesterone drawn, they actually did ovulate. I think the biggest thing to look for is a temp shift. If you can see one then you probably o'd. I don't know that even the best experts would agree on o dates so I try not to split hairs on things. My chart, I think FF has marked correctly even thought it doesn't follow the three over six rule. But I am going to do an experiment and see when I test positive (well if I test positive that is! LOL). If I don't test positive when I think I should, I am going to consider that my o date was off and go by the three over six rule and change my o date.