Please see the attached model.
You should use the PWM Out component for generating PWMs with the RT Box. With the Digital Out component the output can only change once per model time step. With the PWM Out component the output's are generated by the RT Box's programmable logic and can change state between model steps. The PWM Out component also has a configurable dead-time setting.
For a control applications, generally the model step should be synchronized with the PWM generation as configured in the PWM Out component. The step size is then set to an integer multiple of the PWM period.
The following video on the Plexim YouTube page might be informative: https://www.youtube.com/watch?v=8cRU65tga-s