I think it depends on what accounting system you are currently using, and whether or not you are going to be flexible with it. For example, suppose you are using QuickBooks and you want to continue to use that. Your options as to what will tie in with the QuickBooks API are going to be limited compared to, say, if you had the flexibility/resources to build an accounting system from the ground up to tie in with your online store.
At the end of the day, it really comes down to what your resources are like. If you have the ability to build something from the ground up, you can create a really awesome super-integrated system that does the eCommerce store side and also the backend accounting side. If that's not an option, then try to find an accounting system with a robust API that will work with whatever programming language you are using for the store.
Dani
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