Welcome aboard, Rick. A couple general responses first and one specific one... If you've got a multi-system setup that does exactly what you need, then I'd say go for it. The only real "pitfall" would be in forgetting to update orders in Ubercart once they've been processed so that customers never realize their order was received and any on site workflow stuff doesn't get fired off. So really, I'd say any sort of integration can work if you have a good enough system and the sales team works with it.

We use QuickBooks right now for our accounting, and we have a separate homebrew inventory system. Granted, a lot of the rationale behind Ubercart was we needed to consolidate our systems. Doing some contract work a couple months ago someone asked me to look into PostBooks integration, and my thought at the time was that it would be extremely difficult in the absence of any solid importing process. With QuickBooks we can connect to our company file through a web service, so I whipped up a web app that takes care of the integration. With PostBooks, the best I found was a manual CSV importer, and I was never really even able to test it. Part of the problem was I didn't have a local copy to toy with, and I'm also unfamiliar with PostgreSQL. But the bottleneck still seemed at the time to be no good way to get the data in. For your purposes, you might start with the EDI module I wrote to export data into CSVs, but I don't have any good ideas on getting it into your PostBooks company file.

If you do come up with something, though, I'd love to hear about it.