I would try some OTC allergy meds like Claritin or Allegra. If you can afford to (sort of pricey at $20 for a 2 week supply) I would get Claritin-D or Allegra-D. They have an antihistamine as well as a decongestant. You have to get them from a pharmacist (behind the counter) and show your ID.
I take Claritin-D daily for the same symptoms you have. I get bad headaches at night and my nose gets stuffed, with sneezing and runny eyes. Since starting Claritin-D, I no longer have that problem unless it wears off before I go to bed. I now take the 24 hr so I don't have that problem, but when I took the 12 hr, it would always wear off before bed and I'd bee all stuffed up.
You might be possibly suffering from allergies. Have you tried taking any sinus medications? I sometimes have this problem and I take medication for sinus pressure/headaches.
i suffer from migraines too and i typically get them at night i think its because of your body enduring all of the stress from the daytime.. you could have a sinus infection too which couple explain the stuffy nose when laying down??