First off, people... NEVER EVER EVER FLY WITH A COLD. What happens is your eustachian tubes (the tubes between your nose and ears) get blocked, your ears can't pop which is how your body adjusts itself to altitude. So the pressure builds up inside of your head. IT'S VERY DANGEROUS. I am not at all even slightly kidding.
It could take a while to clear out, depending on how bad your sinuses are. If it's been two weeks, that's a clear sign of infection, you should go to a doctor, he'll give you amoxicillin, and you can clean the sucker out.
If you want to avoid it in the future with the least amount of hassle, just take a sudafed or any other nasal decongestant, especially if you're flying with a cold.