It sounds like you might have cluster headaches. My friend gets them pretty bad. She told me that when she gets them that it is only on one side of her head and her eyes water and get swelled up and puffy like. She also says that her nose will start running on the same side. She has always had issues with migraine headaches. SHe says that sometimes she will wake up in the morning or from a nap and she will get the headaches.
She went to the doctor and they prescribed her some pain killers and scheduled her to go to the neurologist. She is going next week. I will try to come back and let you know what they said about them.
I would advise you to go to your doctor and tell him about the headaches you are having.