You would have to file a petition with the court, but especially if he is in agreement, you should be able to get a judge to agree to a name change.
You will have to file a formal Petition for Name Change in Court to effectuate this change. You would need to file in the same county that your Paternity Acknowledgement was filed and established.
Where was the Order establishing paternity issued? If he is consenting to the change, then it will be relatively straight-forward. I suggest you contact an attorney for a private consultation to discuss the costs of such an action.