It looks like you tried to include a picture in your post. Unfortunately, it didn't come through. Could you please try again to add the figure?
Speaking generally, with the TI C2000 Code Generation the PWM outputs will always be a complementary PWM pair on ePWM1A and ePWM1B with the specified blanking time. To have a truly independent second PWM channel, you can simply use a second PWM output. That is, use ePWM1A and ePWM2A, and not connect the complementary signals.
You also have the option of modifying the generated code to configure the ePWM Action Qualifier registers as needed, but note there will be a disconnect between your PLECS model and modified code unless you modify the offline model accordingly.