Rex, I also use Crowe Chizek's Automated Workpapers program. It is a Lotus Notes program. It has been a huge benefit to us. Crowe populates the database with their requests well in advance of any visits to our bank, and as items are completed, I post them to the database for Crowe to review.
AWP has eliminated a lot of emailing that used to take place. There are fewer surprises when Crowe arrives at the bank because the requests are normally all posted to the database ahead of time. They are able to do their work more efficiently when they are here because I've already provided most (not always quite all) of the info requested on the database before they ever arrive, so they can review it ahead of time.
Another benefit is that the info from previous years remains available on the database (although it is eventually locked after it is reviewed, so that no changes can be made). This is often a quicker reference tool than going back through all the info saved on my PC if I need to refresh my memory year to year on how I did something.
As for weaknesses, the only problem we have had is that you must "replicate" your data to a shared server (if I understand how this all works--not a "techie") and during Crowe's busier times, there can be some delay between the time I post on my end and the time they can see it on their end, and vice versa.
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If ignorance is bliss, there ought to be more happy people.