Has anyone used both? What are the main points to keep in mind?
For small businesses (where it's just you and possibly a few employees), they typically use inDinero exclusively b/c they don't have complex needs.
For larger businesses (more than a few employees), we actually see a few customers on both inDinero and QuickBooks simultaneously, where the business owner will use inDinero, but they'll also have an accountant on QuickBooks.
In any case, it completely depends on what you're looking for. Accounting software like QuickBooks was built with accountants in mind, so many of our customers are converts. Feel free to email ceo [at] inDinero.com, and we'd be happy to give you the complete low-down.
If you need to keep a business' finances in order, prepare for tax allocation, keep track of P.Os, etc, InDinero may be a piece of the puzzle.
As you've stated you have a CPA who prepares your financial statements (I'm assuming). They use Quickbooks so anything that doesn't export to that is kind of a waste.
Indinero, Less Accounting, Xero, there are a lot of products out there that claim to do business accounting easily. Mint.com works very well too - the question is does Indinero have the feature set you need at the price you want?