The Werewolves did operate behind allied lines during the war and a little bit after it. However, there wasn't much success with it. Part of the main reason was as you said there was no organized leadership. Also, the German people were tired of the war. All the young men of military age were probably off fighting somewhere in legitimate military units, and if they survived they either were captured at some point or tried alluding captivity. Starting a resistance partisan movement against the Allies and Soviets was unrealistic. The Werewolves were also somehow tied to the Volkssturm. So they were competing from the same pool, old men and young boys. The teenage boys were the most reliable, because they were truly enamored and indoctrinated by the Nazis. However, at the end of the war the allies had such a strong military presence in Germany, and the German people were truly fed up and tired from war, that they just had no more will to fight. They knew they were defeated and conquered.