I know exactly what you mean because I have the same problem!
One of the things I use to explain is:
1) am/is/are and do/does (or other tenses) are helping verbs, I don't use the term "auxiliary". These verbs help other verbs most of the time; the helping verb Do/Does helps all verbs in the Present Simple. But BE does not need a helping verb!
In questions or in negative sentences, when the main verb appears in its base form, DO/DOES will help it:
DO you LIKE chocolate?
and we never use AM/IS/ARE together with the base form.
2) - AM/IS/ARE will help other verbs in the Present Progressive:
ARE you LISTENING?
- AM/IS/ARE are also followed by adjectives, adverbs, nouns:
ARE you HAPPY?
IS she AT HOME?
IS he YOUR FRIEND?
The best thing to do is repetition through substitution drills, like, for example:
You say a question and a substitution: Do you like chocolate? (they)
Your pupils must say: Do they like chocolate?
They: Do they eat chocolate?
They: Does she eat chocolate?
and so on... After drilling well the questions with DO/DOES, switch to AM/IS/ARE.
When you feel they are ready (after 2-3 lessons) then mix both auxiliaries; this is difficult, but possible.
and last point: students must be exposed to the language as much as possible. You can spend hours explaining to them all the theory and grammar, and they won't be able to use it fluently when practicing conversation. But, if they hear you asking them correctly, or if they listen to recordings of dialogues, and finally, even listening to songs written correctly, they will internalize the patterns.