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?
2002: 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.
- NetLedger/NetSuite is not fun
- Microsoft GreatPlains Dynamics is good is you can find a good ASP host
- Intacct is a good/flexible pure-cloud offering
- bought by Sage in 2017
- 2018-2019 co-workers going through migration from QuickBooks, not apparently a friendly API to work with, have to wait for consultant to build pieces.