Here's a useful trick to help you keep the Main Character and Protagonist separated in your thoughts. Refer to the Main Character by his or her proper name: Dorothy Gale; Michael Corleone; Rocky. Refer to the Protagonist by its role: the girl from Kansas; the youngest son of the Corleone family; the wannabe boxing champion.

• In The Fugitive, Dr. Kimble is the Main Character and he is concerned with finding his wife's killer. In the Overall Story throughline, everyone is concerned with capturing the "fugitive" convicted murderer (the doctor) and putting him back on death row.
• In Hamlet, Prince Hamlet is the Main Character and is concerned with the loss of his father and how his life has lost its rudder because of all the recent changes. In the Overall Story throughline, everyone wants to forget about the unfortunate circumstances of King Hamlet's death and move on...if only that son of his would let them.
• In Star Wars, Luke is the Main Character and feels stuck in his adolescence--he's meant for bigger things. In the Overall Story throughline, the Rebellion has stolen the Death Star plans and hopes to use them to find a flaw in the planet-killer before it wipes them out.
• In The Silence of the Lambs, Clarice Starling is the Main Character and is haunted by the screaming of slaughtered lambs (and has transformed that drive into protecting the "lambs" of the world from "wolves" like Hannibal Lecter and Buffalo Bill). In the Overall Story throughline, the serial killer, Buffalo Bill, has kidnapped the Senator's daughter and will kill her and others if he is not stopped.
• In Garden State, Andrew Largeman is the Main Character and is concerned with his health (short but blinding headaches) after a lifetime on lithium. In the Overall Story throughline, everyone is concerned with reconnecting with the "famous" actor ("Hey, aren't you that retarded guy on TV?") after his mother dies and he returns for an extended weekend to attend her funeral.