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 Here's a real answer, sbimn. You've just run into the combination of people appalled by the low level of competence some of these "professional to professional" questions show - we're afraid for the tax payer - like a doctor, if you screw up, the "patient" can end up in terrible shape. And, the fact that everyone on these boards generally charge for professional assistance beyond "simple" questions and have every business persons right to protect both their profession and their "market share". That said - I help people get their businesses off the ground, and you get one of my rare "freebies", to clear my head for the more serious work on my desk that I am currently avoiding while my head clears up from a series of workshops and meetings.

You should define precisely how to carry out the following processes, depending on your preferred resources:

Logging in: Have a system for logging in all the clients so that at any time you know whose papers you have in the office - you're legally required to return any original paper on request - you're under no requirement to give over finished work, before payment - and I suggest a house rule that no return leaves prior to payment. This can be a formal log or an appointment book that always says who came in, their phone number and who took the interview or file, and is always updated for no-shows. Your own work papers and copies of the client material form the basis of your legally required files and you do not ever give them away or destroy them for completed returns, in less than the legal limit for retaining files. 

Files: Many people keep their files electronically - I have a bias towards paper. I'm also lazy and now that my fax/copier/ scanner has a sheet feed, I scan back-up paper to a pdf file. I save constantly (auto save is set to every 10 minutes) and back-up all electronic files at least daily because I hate to redo any work. I do not believe computer and internet security is good enough yet so I back up to my own extra drives and regularly cut archive CDs - storing them properly labeled by year in a locked cabinet and preferably password protected so that a thief steals junk. 

Make sure that your computer housekeeping has a clear back-up and working folders schema so if someone has to take over work on a file it is clear where all the data is. I keep actual photocopies of all 1099s and w-2s, and the actually used final refinance total sheet for every refinance of personal or business property, for currently deductible and basis calculations. Also, all client submitted work papers and total sheets, and preparer created worksheets and excel workbooks - ALWAYS labeled clearly with the date, including the tax year and year created and the worksheet filename. 

On excel and other electronic worksheets, I require a footer that always contains the filename so all printouts can be referenced to the actual spreadsheet that they are printed from. I also require that spreadsheets have named tabs, not merely sheet 1, sheet 2, etc. and the tab name is also in the footer. So footers are always present and include filename, tab name and page number. For electronic files I keep a scanned, multi page pdf of the paper file, which can be printed in part or whole as needed. Those who wish can now retain only the electronic version but I have found over the years that it saves me hours of time and I'm able to deal with a variety of unexpected issues - long after the TP has lost or shredded their own paper. They also get trained to collect and keep everything I require to always be able to prove that my work was complete, legal and excellent. I also always leave a mark that's clearly mine on the original docs I view, before returning them, so I can never be told that I "missed" something when in fact I was never given the information. 

Paper never crashes, goes out with the power, or refuses to run on a new computer, and it's easy to scan quickly for prior year info, and to track backwards through the years for long term issues such as sale of business property, or a long held personal property which may be converted or sold at profit. Every business needs file drawers and I don't have a problem with having them. In consultations, multiple people can easily reference the files, telephone questions can be quickly and easily answered, I don't have to close any files I'm working on to double check things, someone else can discreetly show me the paper and answer for me, so I don't have to obstruct my current workflow, and more.

Logs, files, audit. Everything should be run through a separate audit process, preferably by someone who knows nothing about the file, and can look at it with fresh eyes. Every line item and number should be checked for accuracy, w-2s and 1099s, etc. should be be separately totaled by calculator to ensure against those simple errors that are trickier to spot like dyslexic numbers. The total file should be checked for tax law errors, entry errors, common program errors like checkboxes and new worksheets that don't flow through, and an error list should be created and the file rejected to the original preparer for correction. This will sharpen people up at the beginning of the season and training meetings can remind people to watch for common errors in their own work. Entry errors can be fixed easily but tax law errors mean either your staff needs better training or someone may not be suited for the work.

Training. I do not consider the regular required trainings (in some states) of 60 or 20 hours to be in-depth or complete enough. Hold face to face trainings of all preparation staff including non preparing support staff. Prior to beginning the season go over all tax law changes, and new software updates issues. Encourage comment which will encourage prior study. Throughout the season hold brief updates on issues that crop up - again face to face so that everyone really is informed and has no excuses.

Again, I keep paper, or at least a pdf containing copies of the paper, for every number on every actual tax form. For any big number I keep the back-up paper for the detail numbers that went into those numbers, and I require liberal use of statement lists that detail the numbers in the tax return file, rather than just undefined totals. This helps prevent returns from getting audited in the first place and helps find where to get a positive change if there is an audit. I require the file and papers returned to be in order, and stapled together so the client is less inclined to remove things from the bundle, then claim I missed something. The order is w-2s, then all 1099s grouped by type, business income, k-1s and rental 1099s, in tax return order - b schedule, d schedule, etc., income first, then expenses, these originals are returned to the client, stapled in order behind the stapled client copy tax returns in the same folder/envelope, and for my files - then my work papers, then the client work papers -- tax return in front, papers behind, in order of year - current year and backwards.

Paper file maintenance - I pick a color for the years new files and keep a color chart which tells me the year the client first came in. I place a new year sticker over the old one every time the return for that year is completed and in the file, so I can tell at a glance clients who still haven't come in - and use slow times to give them a call and hurry them up. When files start getting too fat I pull out the extra copy and shred from the oldest closed years and here discretion is required. I don't need the old w-2s and 1099s unless there have been odd issues but I keep the basis calc papers and much of the business paper if there is any chance the client may become subject to a deep audit. I clean out very carefully and only if I really need the space based on the "better safe than sorry" principle. I hope this helps.