I do not know where you live, but in Canada you can go to court and file an Application Order for Variance. This is the first step, and your ex has to be given notice and a chance to appear and dispute the application.
Then if she makes no attempt to dispute it you can get the change made.
Again in Canada custody cannot be passed down via a will. What you can do is put in your will that your parents or whomever become guardians of any minor children. Then the guardians can apply to a court to gain legal custody, but this is not needed as the fact that you have appointed them guardians is sufficient. You need to get the custody issue solved while you area alive so that if you do die and the children are still minors your ex cannot come into the picture and screw things all up.