i know you obviously have googled H bridge circuit so you understand exactly what the pwm mod if for, but as a refresher lets take a look at a basic H bridge
look at page 116 of the datasheet for the chip, you will see that first mode 1 pin modulates ((turns off ((pwm)))
so that mode is no good because only one colour will be under pwm control
next mode
now this is half bridge mode, almost looks promising, because you get two modulated out puts YAY problem solved you say! BUT NO, look at the diagram in the datasheet page 116 figure 13.4
in half bridge mode when one pin is high the other is low, this is for running a half bridge, look at the diagram above work out how it functions.so if you used half bridge mode only one colour would be on at a time then another colour on, they would never be on at the same time that is the point of this mode
next mode full bridge mode forward. now in this mode you would get one colour on as in no duty cycle it would just be on one other colour would be off completely off and the other would be doing want you want i.e it would be modulating
next mode is full bridge reversed wich the exactly the same as forward only reversed!
so as you see 4 outputs with just one pwm mod is as useful for simulating a candle as a circle is for drawing a straight line!
yes you have 4 outputs no they dont modulate at the same time no you cant make them into a candle.
study that drawing in the datasheet then look at the H bridge circuit and figure out what each mode does, a clue a pnp transistor needs to be logic 0 to conduct and a npn transistor needs a logic 1,
and that is exactly what that pwm unit is meant for, it is designed to run a motor forwards and backwards, it dosnt at any point have 4 or even 3 modulated outputs at the same time and the only time it has two outputs modulating they are not doing it at the same time they are designed to run a npn and pnp transistor at the same time,
it dosnt matter how good your code is you CAN NOT GET THOSE 4 OUT PUTS TO DO WHAT YOU WANT TO DO WITH THAT UNIT!
YOU WOULD NEED AT LEAST 3 PWM UNITS NOT PINS OR OUTPUTS.
go ahead write a simple code to use those 4 settings at best you will get 2 colours flash one after the other, if you choose red and blue you get a ace police car effect!