The simplest way to achieve this would be to just have the thermal drift at the same horizontal velocity as the wind - and then draw the cloud above where the thermal ends up at the calculated cloud base.
As you know this is not entirely realistic, because thermals have upward momentum and thus tend to drift with the wind a bit slower than the prevailing wind - the reason it’s much easier to fall out of the downwind side of the thermal and why the occasional extension of a circle upwind is a good idea.
But, for the sake of making it possible, rather than perfect - just trigger thermals from the terrain, have them drift with the wind and then draw the clouds at the top of thermals. This will mean the clouds will drift with the wind.