I was helping a friend evaluate the Oracle Small Business Suite (most basic version of NetSuite) as a combination shopping cart and hosted accounting system. Alas, from the standpoint of a very small business of two or three people, this product strikes me as a total pig, overwhelming, confusing, and unusable.
I wondered if there were any good alternatives. A few years ago, PeachTree had such a product, in partnership with some other company, but it seems to be gone, and they offer only hosted accounting now. Intuit has a hosted version, but also no web store attached.
Our accountants use a hosted server-client system but I'm not sure of the specs on it. It is probably not appropriate for what you are doing though.
Have you thought about potentially separating your accounting software from your online store processing and merely merging or importing the online store records on a daily, weekly or monthly basis?
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I'm working on exactly such a system myself. Webshop, Invoicing and Accounting system integrated into a single web-based application. It will be easy to use and not include all overhead of larger packages. And the package will be relatively cheap.
However, the system is still by far not ready. We hope to have the entire package ready around September, with smaller packages released earlier.
I would like to post more information on the system, but that would be an violation of the TOS. So if you have any questions or request, just contact me by email.