They need the general rule that English verbs can be verb phrases, which have an auxiliary or modal like "have" or "do". And that such verb phrases inflect the auxiliary verb, while the main verb stays in the infinitive form (or in the participle form, as the case may be). The auxiliary carries the tense, negation, person and number.
Also it helps to imagine that there is always an auxiliary. If you don't see it, it is invisible, but still there. When the auxiliary is invisible, it cannot take the tense, number and so on; these markers go to the main verb.
Now when you make a question, the auxiliary and sentence subject exchange places (subject-aux inversion). This still happens when the aux: is invisible.
Visible aux (will):
Statement: You will have the soup.
Question: Will you have the soup?
Invisible aux:
Statement: You [invisible] have the time.
Question: [invisible] you have the time?
But now, this invisible aux is dangling up in front of the clause and that is forbidden. In this situation, the invisible aux is instantiated in a visible form, and it appears as the verb "do":
Question: Do you have the time?
And, as usual, this invisible-come-visible aux now takes the tense, number, person, "not" negation away from the main verb. With that we can more or less semi-accurately understand how "do" works in forming questions.
Remember that the mistake I mention above is often made by beginners. While it is true what you said, it is easier to just tell them: always use two verbs in a question or negative sentence. If you don't have two, just borrow "do" and apply the appropriate time/person to that verb and use the infinitive form of the second verb.
When learning a language it is important to have easy-to-understand and simple rules. When you try to write or speak in a foreign language, there are a lot of things to consider and you are going to forget a few. The best thing you can do is practice a lot until it starts to sound natural. If you always try to apply all rules you've learned, you are going to miss some, no matter how smart you are. It's also important to have someone who can correct you and tell you the appropriate rules.
Also it helps to imagine that there is always an auxiliary. If you don't see it, it is invisible, but still there. When the auxiliary is invisible, it cannot take the tense, number and so on; these markers go to the main verb.
Now when you make a question, the auxiliary and sentence subject exchange places (subject-aux inversion). This still happens when the aux: is invisible.
Visible aux (will):
Statement: You will have the soup.
Question: Will you have the soup?
Invisible aux:
Statement: You [invisible] have the time.
Question: [invisible] you have the time?
But now, this invisible aux is dangling up in front of the clause and that is forbidden. In this situation, the invisible aux is instantiated in a visible form, and it appears as the verb "do":
Question: Do you have the time?
And, as usual, this invisible-come-visible aux now takes the tense, number, person, "not" negation away from the main verb. With that we can more or less semi-accurately understand how "do" works in forming questions.