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[Edit: if you need superb inventory control, you'll need QuickBooks Pro.... AND there's now a version for contractors of the build-a-house type, but which is what I use for my web business.]
There are two distinct issues:
1. How to abide by the regulations
2. How to make the most of the regulations.
For me QuickBooks will satisfy the first, no question about it!
For the second you need a very good tax attorney. Not easy to find!
Either way, QB is now the accepted standard for accounting, especially if you are USA based :)