Hi S R,
Thank you for your answer. Actually, I have seen some examples in the path you've given me. However, I found it very tricky to incorporate those steps into my VI. I don't know how to verify whether Ctr and AI from the same card and different cards are synchronised (after trying to follow some ideas from the examples).
You mentioned about "array manipulation". As you might have seen in my code, there are different sizes of arrays (Ctr and AI). I'm not too sure if the synchronisation of those signals are badly affectly by this (of course, I didn't use any trigger or share any clock source among different signals, but if my understanding is right, there shouldn't have big delays of time between different signals).