Let's go back to the beginning. I'm not clear whether or not your Council has appointed an Internal Auditor for the current year. Most will have done so by now, so this is an unusual time to be addressing this, unless your previous auditor's circumstances have changed. If you are appointing someone now, this must be a full Council decision, based on information provided to the Council by the Clerk and/or the Chair etc.
Your Council has employed a Clerk to deal with all correspondence, amongst other things, so routine correspondence with the Internal Auditor is the Clerk's responsibility. As ClerkinEssex has stated, there would normally be virtually no correspondence, so what has prompted your question?
Next summer, your Internal Auditor must sign a statement confirming that the Council has operated in full compliance with the relevant legislation and the Chair, on behalf of the Council, must sign a similar undertaking. There is very little room here for a Clerk to influence the proceedings.
Finally, a good Council functions on trust and respect, so any of my Councillors may see any item of correspondence received or sent at any time, without question, unless prohibited by legislation, in which case, they receive a verbal account of the matter.