Terry - a few things I've learned over the years concerning clients and Quickbooks include keeping the chart of accounts short and sweet. Lots of clients come to me with pages and pages of accounts on the COA. That makes for lots and lots of opportunities for coding errors, IMHO. But, as long as the QB type is correct (expense, income, asset, liability, equity), the data errors are manageable.
I might suggest that you perform your work on a monthly or quarterly basis since this also has worked better. The bookkeeper will probably be able to ask and answer questions as the issues are more recent than looking back annually.
Also, I don't think trying to force QB to a strict tax accounting basis is going to work for the reasons you mentioned above. I think you can figure the AAA, etc. from preparing the tax return. Again, I see no benefit to angsting over AAA, OAA, and AEP if the company has always been an SCorp. I have only needed to consider the ordering rules when the shareholder takes distributions in excess of basis, and I keep track of that via the shareholder basis worksheet in Drake. You might be making the bookkeeping in QB a lot more difficult than it needs to be. My own philosophy is that simpler is better. I am a simple woman