JarvisSong:
I'm using an Arduino Due to count and send out pulses. The sending out pulses are suppose to last for 1000 microseconds. How do I keep counting the incoming pulses at the same time?
This is confusing.
You say you are sending out pulses and then you say you want to count incoming pulses. Which are you doing - sending or receiving?
The demo Several Things at a Time illustrates the use of millis() to manage timing without blocking. It may help with understanding the technique.
Have a look at Using millis() for timing. A beginners guide if you need more explanation.
...R