Instead of waiting until the pressure has built up to such an extent that they hurt when you pop them, as soon as you are aware of the plane descending (or if you feel a slight buld up in pressure before this) pop them by pinching your nostrils shut, close your mouth and blow gently down your nose.
This is the valsalva manoever and is by far the easiest way to equalise the pressure in your ears (similar to diving). The longer you leave it before popping, the greater the pressure difference between your inner and outer ear becomes and the more distorted your eardrum gets. It's this distortion that causes the pain.