The way I read your post, in the past the (externally generated) "internal" audit report comes in, lands on the Internal Control Officer's desk, and he disseminates it to the appropriate managers for corrective action and then takes the report to the board. If you are going to go with an in-house internal audit, the Internal Auditor needs to issue the report to the manager of the area under audit and he also needs to be the person reporting to the board. Until your internal guy has proved himself to be competent, it is probably not a bad idea to have him report on his progress to the CFO or CEO. That way, you have someone on site that verifies that he's following schedule, working well with others (not behaving unprofessionally), etc. The reporting of audit results, and the actual audit work, however must be independent of management if you want some objectivity. Hope this helps.
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Opinions expressed are solely my own.