Need advice on changing name of adopted son

Hi atty, my mom is legally separated with my dad but they're not annulled. My mom had a relation with another guy and after 24 years they adopted a baby boy. The boy is te son of our helper, they just hve a signed agreement regarding the adoption but it didn't pass any procedures/ processes with dswd. My mom and his partner registered the child under their names, using the surname of her partner. They recently broke up and my dad died last february 2013, now my mom wants to change the name of the child to my dad's surname. I know this is complicated and we really need advice on what should we do.