ANSWER:
Make ruqyah on both of them separately. Ruqyah is done for cure. For protection, you must recite the prescribed daily athkaar.
The Du’ah that protects them with the will of Allah is the one you say in the morning and in the evening which starts with: اللهم إني أسألك العفو والعافيةفي الدنيا والآخرة، اللهم إني أسألك العفو والعافية في ديني ودنياي وأهلي ومالي، …. Allahumma inni as’aluka al-‘aafiyah fi’l-dunya wa’l-aakhirah. Allahumma inni as’aluka al-‘afw wa’l-‘aafiyah fi deeni wa dunyaaya wa ahli wa maali…. (O Allah, I ask You for well-being in this world and in the Hereafter. O Allah, I ask You for forgiveness and well-being in my religious and worldly affairs, and my family and my wealth.
This Du’ah will protect the children as well with the grace of Allah as Shiekh Ibn Othaimeen says. You can also make the Du’ah of Ibraheem when he used to guard Ismael and Is’haq peace be upon them all with: أعيذكما بكلمات الله التامة، من كل شيطان وهامة، ومن كل عين لامة .. ‘U’idukuma bikalimati-l-lahi t-tam-mati min kuli shaytanin wa ham-matin, wa min kuli ‘aynin lammah.