Creating an Internal Audit checklist as per the company's requirement is best way of ensuring that u are emphasisng the checks on the right points. just break the company process flow into departments and identify the relevant procedures. once that is done, identify the documents with the procedure. pick up one end ...the starting document, say the customer order and then start moving to the other end, that is delivery of products to the customer against that order. in the process u cover all the departments.
similarly for HR do the same thing.
and u have the whole organsation audited.
as far as auditing the Management Reps functioning is concerned, simply take the Quality Manual, and ask some one else who is qualified enough to prepare questions on the basis of the qUALITY manual.
and all that is required is for the MR to reply the questions with appropriate documentation or refernces.
this is the checklist in theory...and belive me very easy to convert into practice, provided u have ur flowcharts showing the working of the company as a whole and in divisional form...plus the job descriptions and written procedures are available on u.