By internal FDA audit I assume an internal audit against 21 CFR 803, 806, 807 and 820 (the USA regulations referenced explicitly by MDSAP). Too much for a single forum post, but if you're trying to select a good auditor they would ask for or infer matters concerning each requirement item on the following aspects:
Is it applicable? If not, how is that justified (and where is that justification documented)?
Was it established(listed intent/requirements/record filing location in the QSR)?
Was it implemented/done? And if so, was it effective and the documented procedure still suitable (do not assume the procedure is truth).
Are the people working on it competent by qualification and training?
If you're affecting conformity to product requirements are you doing so in a validated manner, or verifying them on each and every item?
Was it maintained? I.e kept up to date with changing requirements, interfaces with other changed processes maintained, resources adjusted given changing situations.
Do you still have all the requisite records?
I also suggest requesting a (censored) copy or extract of an audit report of theirs. The reporting style is crucial when it comes to internal company acceptance and demonstrating due diligence.