the internal audit covers your entire program and should be done annually. (2.5.4.1 and 2.5.4.2)
then, you need to have a regular inspection of the plant for the gmps, physical, sanitation, ect (2.5.4.3) It sounds like you have this covered.
I also use the audit check lists to create the audit check list for the internal audit and "regular inspection". There are items in 11 that I do not think are required for the "regular inspection but are intended for the internal audit. For instance, on the "regular inspection" I might look at the water system for anything that looks wrong. However, the review of internal water testing and water reports I would cover in the internal audit. Or, for equipment and utensils I would check the condition and design of equipment on the "regular inspection" but would review specifications for equipment during the internal audit.
on the flip side, I wouldn't inspect the floors, walls drains on the internal audit if they were being done monthly on the "regular inspection".
To make it more confusing. Food Defense, Allergens, etc are in section 2. It seems to me like parts of these should also be included on a "regular inspection"
I also encourage the use of the checklists for developing audits and "regular inspections". They ensure you are not missing anything. However you also need to be aware of what the goal of the audit / inspection is to ensure they are meeting their intended purpose and yet not being over burdensome.
Hope that helps -