Since the Bible says nothing of a pastor emeritus, this is a difficult question. From the beginning of any such relationship, there must be a clear and definite understanding of the roles of the two positions. According to the dictionary, an emeritus is one who is retired from active service, usually because of age, and only retains the title for the sake of honor. If the pastor is the pastor and the pastor emeritus is only a position of honor, then the pastor (in this case, the son) must have the right to make the decisions. If this creates friction, then the pastor must decide whether he is the pastor or not. If not, then he should probably resign.
In grace, I must believe that this is one of the most difficult of all positions. The son is to honor the father. The church naturally honors the father and pastor who probably led the church for many years. The son was probably honored to be asked to pastor and hesitated to lay down the rules of operation with his father at the beginning. Now, as things go the way they almost always will (that is, the son wants to really be a pastor and lead the church and the father wants to hold on to the status quo), friction is created.
In the great majority of these cases, one of the men must eventually go. A body cannot have two heads and operate. And, although multiple elders were found in the New Testament churches and are proper, there still must be a head. Otherwise, there is continual confusion. Jesus said it another way: "No man can serve two masters" (Matthew 6:24). I pray your situation works out alright, but I fear it is a very difficult one. When the friction is already known to others (like you), it has gone way too far. Please hold them and the church up in prayer at this time.