When it comes to yes, no questions the student has difficulty understanding why auxiliaries are different for the third person and why auxiliaries vary according to the form of the question. One can try to explain the situation without getting into the etymology of the language and that id by explaining the type of words around the auxiliary used in the basic question.
If one is asking about a certain quality than an adjective is used after the verb as in, "Are you busy?" Here the word busy would describe how the person is, in the statement form of the question, "I am busy" Similarly past-participle adjectives can also be used with the same question to ask about a certain state as in "Are you tired?"
Other auxiliaries can be used like will, may, should, and their past forms to ask about a person's intent, ability or what he is has to do, respectively. So a question like "Can you swim is going to confirm the person"s ability to do that sport but the speaker will change that auxiliary to will to confirm the person's future intent.
When confirming an action expressed by a regular or irregular verb, do is used before the subject of the question as in "Do you swim on weekends?" The person has to learn that whereas the auxiliaries like can and will do not change in their structure depending on the person who is being talked about, "do" changes to "does" for the third person singular.
The do becomes did when asking those same questions in the past as am becomes were when addressing a question regarding identity in English. So "Do you read newspapers?" would become "Did you read newspapers?" and the listener know that he is being asked about a past habit and not a current one.
