BLDC Motor PWM commutation scheme
TLDR: Both control schemes will work to drive a motor. 


first: very simple, not as efficient 
second: a little more complex, more efficient


The First image is a very simple way to drive a motor and allows you to not have to worry about "shoot through" on your half bridge. "shoot through" is when both the high side and the low side of a half bridge are on shorting your supply to GND. this will usually blow up the FETs or the supply. The problem with this simplicity is that when the high side is being PWMed the motor will want to pull current when the high side FET is off because of the motor acting as an inductor. The motor will pull this current through the diode on the low side FET. this will cause energy to be lost in the low side FET diode. This causes inefficiency and heats up the low side FET.

The second image is how most motors are driven because it is more efficient. the image shows that you are not just PWMing the high side FET but applying the opposite of the PWM signal to the low side FET. This means that the when the high side FET is off the low side FET is on meaning that the reverse current does not have to go through the diode and waste energy. One of the problems with this control scheme is that you must add a delay between the high side FET being one and the low side FET being on to prevent "shoot through".this delay is called "dead time". It is usually a very small amount of time 100's of ns though. most motor driver IC's will introduce this dead time for you.