Don't worry, the inspectors know that you are only doing your job and as long as you try and give them everything they ask for, or explain why you haven't got something they ask for, they should be pleasant, professional and understanding.
There are some useful pointers here, although not much in relation to CIS. With CIS, apart from the obvious (checking you have copies of in date CIS cards, the right ones for the payments you are making etc.) they are looking for subbies who may be avoiding tax so expect them to cross-check some payments with their records of your subbies. They will also look closely at the amount of materials on payments made with deduction of tax to check the amount of 'labour', and therefore tax, is not understated. This also applies to payments you are receiving, so they will check your receipts from your main contractors/employers too.
Late PAYE payments will incur interest, but they already know about those so that is not what they will be looking for.
If they find a problem, they will try and work out how much tax should have been collected that hasn't been. They will then issue an assessment on the company for this amount. Your accountant should then argue with them until a more reasonable figure is reached .
I am going to stop there, because I don't want to worry you unnecessarily - remember it is your company's directors responsibility to pay the right amount of tax, not yours, and because hard working managers don't usually prioritise admin., it is impossible for you to produce information you don't have.
Good luck!