It has occured to me that the flickering will effect the fade in/out function, which just wouldn't look right.
My first thought on how to get round this problem is to use a second pin that bypasses the flicker LED:
All well and good, but how does one name a second led pin when declaring its function?
For the flicker LED I have:
int ledPin = 5; // flicker led to mosfet gate
Is it as simple as naming another pin as a led pin (eg. int ledPin = 6; )and then just call that number when it's wanted?