"to make sure" parallelism and comma

Your placement of the comma in the first version is fine. What is not fine, however, is the wording of the sentence:

To make sure that the audit will go smoothly, and you will avoid future questions from auditors, please . . ..

First, get rid of the that; it's not needed.

Second, make the two parts of the sentence more closely parallel by adding an infinitive to the second part. So,

To make sure the audit will go smoothly, and to avoid future questions from auditors, please [answer the following questions to the best of your ability].

Technically, the first comma is not absolutely necessary, particularly if you shorten the sentence even more, as in the following suggestion:

To make the audit go smoothly and to avoid future questions from auditors, please [answer the following questions to the best of your ability].