Which side to do the PWM in a H-Bridge, High side or Low side?
I believe the low side is better because the required N-channel transistors are cheaper and faster than similar P-channel transistors. Switching speed is what you need for PWM; if switching is slow, the transistors will dissipate more energy.

Unless the datasheet states otherwise, don't rely on the internal diodes in a MOSFET. They are not designed for use as flyback diodes.