Is your son born here in Qatar? if he is born here,you need to make a passport for son first then you will need 3 passport you, your wife and a third party (any of your relative or friends) for CID in Industrial Area. You will come back maybe 1-2 weeks in CID and they will give you the passport of your son to make or process the visa in Immigration. There you will bring the parents copy of Resident ID and passport. When the visa is finish you will return to CID to show the visa and then take the other passport.