Back in early Heavensward I really wished that Thundercloud procs refreshed AF or maybe just added 3s to both your stance and Enochian timer or something so that it was never self-sabotage to use them. Nowadays, our timers and general job mechanics are generous enough that we can pretty much always fire off our procs without regretting it. It sounds like the OP just hasn’t learned good rules of thumb for proc use, so they’re getting frustrated at what appear to be conflicts between Thundercloud and Enochian.

Generally, DarkMagician, you’ll want to release your Thundercloud proc when either it or the enemy’s Thunder III DoT is about to run out. As long as your AF timer has like 6 seconds or more on it when you do this you should be able to follow up with either Fire or Despair and keep all your plates spinning. My favorite thing to do is to use Thundercloud or Firestarter when I have either 4400 or 4000 MP left, because I can activate Triplecast during the global cooldown and then cast F4, F4, Despair at instant speed and therefore a substantial time gain.