As far as i know, you don't.
You can use PWM very well for this setup, but it will not do what you seem to think it would do.
PWM is typically used as current control, and you can do that here.
Send the PWM signal(s) to "1,2 en" and "3,4 en" pins.
The outputs are now PWM / current controlled.
To smoothen the movements of your motor, you need to make smaller steps.
And of course check to see if you are controlling the steps correctly and there is no interference controlling your H bridge driver.
So you only lose and dont gain anything with PWM and a stepper.
I thought I would gain some smoothness, wouldn't I? Right now with a turntable and an object on it, when the motor makes one step, it is so abrupt, that the object on the turntable jumps out of position. )
What is the degrees per step of your motor? If it is 3.6 degrees per step it will be jerky no matter what you do. I have heard about new and better driver chips that have half step and micro step but haven't any experience with them.
There shouldn't be any kickbacks and the jerks should be very small if the motor is working properly. I realize the small jerks may not be acceptable, but I get the impression from your OP that you are experience rough jerks which suggests the motor is not working properly.
Get it going properly before you consider "extras" to make the rotation smoother.
I doubt very much if PWM has anything to offer unless your system is sufficiently sophisticated to need a limit to the current in the coils. And if so I think it would be much easier to use a specialized stepper driver like the Pololu a4988.
Are you sure you have the two coils wired so that the current flows in the correct direction in each of them?