treebykooba:
...i put the constantly pulsing pins in the void loop, followed by the FSM for the fade in, on, fade out, off ? then after i put the functions that actually do the things i want?
In the demo sketch that I gave you the link for I have been very careful to put none of the detail coding in loop(). Putting the details in their own function makes the coding much easier to follow.
That demo sketch probably does half or more of what you want. You will just need to add stuff to make the LEDs fade.
...R