I've always found this to be a problem for every SmallCo.
Only incredibly over-priced systems support much customization. Lower-end systems like QuickBooks are very closed boxes (though maybe it has possibilities I'm not aware of). Perhaps some in-between system would have a lite API which would allow a custom front-end system to generate transactions in the core system. Maybe NetLedger will get there?
Jon Udell describes the more prosaic annoyances of having to manually process all the dataflows coming into a business, and notes that XML-based Web Services could help, even without standardized schemas, if processed by an Active Intermediary.
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