Ears are really plugged from being sick and stuffy nose. will this go away on the way?

Yes.: Eustachian tube (et) from throat to middle ear is the pressure equalizing mechanism on either side of ear drum. When throat is swollen from allergy or colds, et function is compromised. So when you recover from the cold & sickness, these symptoms should resolve. You could use warm salt water gargles & nsaid's such as aleve (naproxen) to get some relief in the mean time.