Hi picnaut:

you can obviously try to device a software exor the two PWM signal if a relative measure is what you need and then use internal timer to integrate the resultant pulse. Or, you can output exored pulse and use Ms. Newman's method of external analog integration and measure the magnitude...

you can also use a pulse of known duration to charge a cap and use the PWM to discharge it and measure the average voltage on the cap. The resultant value on the cap will of course be the inverse of the PWM duty cycle in this case.

-warrier