If you set a fixed duty cycle of 50% it should work pretty much the same in either mode.
But if you're going to cycle through changing the duty cycle, you're better off using it with
independent mode for driving LEDs.
Look at the attached graphic. Note how signal 0 & signal 1 would make it look like one LED
was on all the time, while the other was off all the time. Complementary mode is for driving
N channel & P channel motor drivers. It's a lot different than standard PWM.
If the duty cycle was say 70%, one pin would be high for 70%, the other would be low for
70% since they're complementary.
Signals 2 & 3 are in independent mode, so the high duty cycle is the same for each pin.
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