Complementary PWM channels Output

I should say that there are two things I'm working on the first is generating three phase quasi-square waves using an inverter circuit and then implementing Space Vector Modulation to produce three phase sinusoidal waves from the quasi-square waves. For the quasi-square waves, only 6 circuit configurations are required in a specific order for a fixed period for duty cycles of either 0% or 100%. Space Vector Modulation however is much more complex than that.

Programming has never been my strong point, and working with this Due is a little difficult for me, but it is much more capable to do what i need it to do than the rest of the boards offered by arduino.