A couple of things to understand...
The middle ear is a closed system, except for one little hole, which is the Eustachian tube. Your outer ear ends at the eardrum, and is basically just a hallway to let in the sound. Then your middle ear begins, in which the pressure is regulated through air entering and leaving by the E. tube. This is the popping you hear when pressure changes...the air entering or leaving. So if you're stuffy and air needs to enter the middle ear to regulate pressure, it can sometimes suck mucous in and plug it up. I've found that sleeping with the affected ear down can help overnight...lets the mucous drain. Keep the sinuses clear if you can, too. Neti pots and sinus rinses are great. Avoid sugar, as this is an inflammatory and can increase mucous production. Milk also increases mucous.
Also, I highly recommend going to a good chiropractor. If you're out of whack, for some reason it can affect your ears. We had lots of ear infections until the kids went to the chiropractor, to the point of having tubes recommended. Never another one after the chiropractor visit.
Best of luck!