As I understand it you are looking for two signals in 'quadrature' (meaning 90 degrees out of phase, probably doesn't need to be exactly 90 degrees for most applications, but it is essential that the two signals not switch simultaneously as that would be 0 or 180 degrees out.)
The standard PWM modes on the timer allow the two pins controlled by that timer to switch with different duty cycles, with the fast mode this is accomplished by switching both pins together as the counter wraps round, then each switches back at its own point in the cycle. This means both switch simultaneously at the start of a pulse. (No good for quadrature)
With 'phase-correct' mode the counter counts up, then down, then up, and each pin switches at a fixed counter value, one way for counting up and switch the other way for counting down. This means the PWM signals overlap symmetrically, making them precisely in-phase.
In fact each output pin can have its sense inverted with configuration bits, so, for instance 180 degrees out of phase IS possible - however its still not quadrature.
So the method RuggedCircuits suggests is a neat trick to get quadrature out of the timer unit - new to me, sounds like the way to go. Study the relevant timer chapters in the datasheet for all the details. timer1 is the most general timer, so I'd start with that one.