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??
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 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.