is there a easy way to pulse a digital output with one of the three timers. If i use delay(?) it pauses the program there. I need a way to do this on it's own thread so it dosen't interrupt the program execution.
You can execute code to adjust the digital output by setting up a timer to generate an interrupt and putting the code in the interrupt routine, but it will interrupt the main loop briefly. There is no way around this. However, as long as you keep the code in the interrupt routine short you will most likely not notice the interruption in your main loop, it will pick up and continue execution where it left off.
One way to do this is with the MsTimer2 library.
Depending on what you are trying to do you might also be able to use the Timer1 library.
Thanks i'll give that a try.