A lot of AMTA auditors ask this question. The way to perform an audit is to first do the empirical evidence based field work, the Documentation Interviews and Observations (DIO's). Doing these will give you percent % compliance for each question but not a final score for the question. If you go to the areas for documentation and observations you will see that you can edit the sites you've visited or people you've interviewed, once there use the dropdown next to the question to score the percentage % compliant (interviews are positive/negative/etc.). This will propagate down to where you're scoring the question and writing the findings, SFI's, etc. At the question level you're to look at the percentage compliance and then manually score the question based on the guidelines. If you ever have the need or are asked to fix (based on QA Review) the % on the question you will need to revisit the Documentation, Interviews and Observations section and make edits to that section. Your percentages will again repopulate next to the question score that you've given for that question. Remember that the percentage compliant (eg. 80%) given in the DIO sections are not the final scores you can give at the question level (eg. 5/5).