Quote Originally Posted by KrayZ33
I think the right question would be "why should it be possible for him to tell the difference?"

from what I know, the clones are physically alike, chakra wise too and even able to think on their own
I would think it would be due to the ability to analyze techniques rather then any differences in the clones - he can see how the technique is working as its activated so can identify each clone as its created. From there its just a matter of making sure he keep track of them. At least, that would make sense to me.