High side N channel gate driver
I do believe that the datasheet schem was not an inductive load so I am guessing that is why they did not have the flyback diodes.


The MOSFETs have 'body' diodes built in, so external flyback diodes are not required. They can be added if you want to reduce heating in the FETs (use Schottky diodes for lower voltage drop). 


  capacitor 5... do I need this capacitor ?


Yes. It reduces voltage ripple on the power rail caused by the current pulses drawn by the motor. It is especially important if the wires between the power supply and controller are long, as their inductance could cause the voltage to spike high enough to blow up the MOSFETs.


  I found some discussion on the capacitors not recovering quick enough... should I pwm the low side MOSFETS instead ?


With this scheme you must PWM the high-side MOSFETs - otherwise they will not turn on fully because with no PWM pulses the bootstrap capacitors will discharge. You must keep the PWM ratio sufficiently below 100% to ensure that the capacitors remain charged whenever the upper FETs are turned on.

If you want a full 0-100% PWM range then you will need drivers with internal voltage boosters (eg. LTC7004), or use isolated DC/DC converters to provide 12-15V to the high-side drivers. Then you could turn the upper FETs on continuously and PWM the lower FETs. 


  will the capacitors recover quick enough with a 480HZ or max
  980HZ pwm ?


At 480-960Hz the capacitors should have no trouble staying charged up because the average charge transferred to the FET Gates is small. However at this low frequency motor inductance probably won't be enough to maintain continuous current flow through the windings, which will cause increased vibration and motor heating. Most motors need a PWM frequency >=3kHz for efficient operation. 


  should I run both channels on the driver at the same time so 3 and 2
  would be on driver 1, and 5 and 4 on driver 2? Or is it fine to run
  the high on one driver, and the low on the other driver like I have
  drawn in the schem.?


To drive the motor you need to turn on M1 and M4 in one direction, or M2 and M3 in the other direction. If two FETs on the same side are turned on at the same time then current will 'shoot through' them and short out the power supply. Shoot-through should be avoided at all costs because it will eventually blow up the FETs. 

When testing your firmware you should use a current limited power supply, or insert a current limiting device (eg. incandescent light bulb) between the power supply and the controller. This will save your FETs if a software glitch causes them to be turned on at the wrong time.

To brake the motor turn on both lower FETs. This puts a short cross the motor so it generates maximum current and braking torque.