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I would suggest to file taxes for the current year first - meant 2007 - especially - if the client have taxes due.
That would be easier to collect all required documents and information for the last year than for previous years. You may file an amended return if needed at the later time.
After that - you may start working on 2006 return - I suspect that you would have issues with some documents and information - so you would need to do estimates. Have client to sign that he/she is agree with estimates and that they would be corrected as soon as additional information will be available - that should be looked as you are helping client to complete the tax return as soon as possible and are not "making-up" any numbers that the client is responsible.
At the same time - you may help the client to set the books - that would be separate task - so at the 2008 tax time - you will be in the better position.