The ONLY way you can be sure that someone with Aspergers truly understands you is to interact in conversation with him/her.  With a tendency to "not see the big picture", they often take things out of context or mis-construe the true meaning of what is being conveyed.  Also, with a tendency toward literal interpretation, teachers need to check for accurate comprehension. 

Many students with Aspergers find the school setting over-stimulating and stressful.  They cope by responding in as few a words as possible.  This serves to end the conversation in quick order.  Responses to questions like, "Do you understand?" are typically answered with "Yes" regardless of whether or not they truly do understand.

In addition, an Asperger student might respond that they positively do understand because they believe that they do; when in fact, they might not.

The only sure way to check for comprehension is by initiating an in-depth conversation on the subject in question.