How do I take one of them off his birth certificate? I went to the court house and they said to talk to the vital records about it, and they now just told me to go to the court house...

A formal name change with both parents signing requesting the change at the court house, it does not "change" the original birth certificate but it does legally change his name and you can get a new birth certificate issued then.

Well the thing is, his father gave me a fake last name when I asked how to spell his last name..