After reading more and more I think I understand what is actually happening. When using registers and pwm, the registers are only turning in the LEDs for a fraction of a second at full power rather than the serial way of tuening them on at a percentage of power all the time. Add in the PWM to regulate (modulate?) the length and frequency of the se periods of on and you can simulate the percentage values.
In essence you are trading a percentage range for a time range and then simulating the percentage range.
If I turn on red channel for 2 units of time and the blue for 1 unit then off for 1 then you can get orange (rather than yellow for both on for 2 units concurrently). If you make the units short enough then the human eye wont notice any discernable changing and think of it as orange. I guess it is like persistence of vision demos.
Presumably the registers are able to handle the fast switching needed for this kind of thing? Same for the arduinos.
Is this what is going on?
The libraries and parts supplied look like really good options. Thansk for the suggestions I'll see if I can get someting working out of them.