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Setting up a company for a consultant or independent professional is fairly easy, and the help and documentation can provide guidelines on what to do. Also, when you get an accountant, Quickbooks exports and reporting is something most are familiar with.
I'm using qb 2006 pro. My accountant has that version among other versions. I was using and older version and he had to spend some (billable) time each year getting things into the format he was working with.