Nice article and lays out the challenges nicely. We have observed this with our customers a great deal. Did you try QuickBooks Merchant service for credit card processing - thats probably another topic of discussion.
Just curious so which shopping cart did you choose finally. I ask because we are in the business of providing QuickBooks integration for many eCommerce shopping carts - http://www.atandra.com/Prod_THub.htm
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I've run into the same issue with QuickBooks
I do osCommerce programming, and the biggest issue with the contributions listed on the osCommerce website is that they are either incomplete, or work partially with older versions of QuickBooks. I did happen to setup one client using QB 2003 with an osCommerce store, and as far I as know, they never upgraded to the newer version of QuickBooks and they seem to get by without any major issues.
The main issue with anything integrating into QuickBooks is their IIF import file format. It's very finicky, so much so that I once tried to load what appeared to be an acceptable IIF file into QuickBooks 2006 and it corrupted my company file (the same file worked inside 2003... go figure). When you toss in inventory control, QuickBooks and many e-commerce systems just fail. QuickBooks will call an item BOB100 and you're store will say it's BOB100-Brown.
We ended up having so many issues with QuickBooks, that we now recommend a product called StoneEdge (www.stoneedge.com). Their Order Manager application is compatible with a bunch of the major e-commerce players and handles the entire order process seamlessly... from downloading orders, to sending out confirmation e-mails, to taking the right number of items out of inventory (online and inside their database). From inside StoneEdge, you can generate a general ledger report that integrates back inside of QuickBooks for your accounting, or you can just print off accounting info directly from the application.
StoneEdge isn't really for the small mom-and-pop store... however if your wife's business grows I would recommend looking into it. For a store that sells a limited number of items, I'd look into ZenCart (www.zencart.com), an osCommerce branch project that includes a lot of additional features out of the box. It may just have what you're looking for (and your wife may like processing the orders from the online interface).
I hope some of these suggestions helped!
QuickBooks Integration Done Right
For QuickBooks integration done right you need the fast, free and relatively easy to use QuickBooks Software Development Kit, The QuickBooks SDK has been available for more than six years at http://developer.intuit.com/. About 500 leading-edge programs make this QuickBooks SDK even easier to use or make QuickBooks far more powerful at http://marketplace.intuit.com/. This is QuickBooks integration done right.
QuickBooks users can work quickly & accurately, while never entering data twice. The SDK avoids QuickBooks data file corruption, which is common with IIF imports. The SDK insures QuickBooks integration done right in ways the IIF does not, since the SDK never breaks working applications when it or QuickBooks upgrades. Most important, Intuit may soon drop obsolete IIF imports from future versions. Therefore, saying you had problems linking QuickBooks with IIF is about like saying you cannot hold them together with a snale.
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