It doesn't really matter...both parents have to sign anyway, as far as I know.
If you aren't together then there's a form you can send to the other parent, have them sign it and you send it in with the passport application. We just recently did this.
There's also a provision for when you can't get in contact with the other parent or if they refuse to sign.
All the form and instructions are on the official passport page. Sorry, don't have the direct link, but you...