In order to have a "custom" applications be able to talk to your scanners, your best bet is to hire some one to write a custom interface that will work with your accounting software and a TWAIN device. TWAIN (Technology Without An Interesting Name) is a standard for getting input from image scanners: an image capture API for Microsoft Windows and Apple Macintosh operating systems.
It's doubtfully that you will fine the solution you seek on this forum.
I imagine it should be possible to develop a Java applet or an ActiveX component that hooks into TWAIN libraries. This would require the client computer to accept, download, and successfully install your custom-developed object.
If you can choose between Java and ActiveX, I recommend Java because it can be platform independent. ActiveX is IE and Windows Only.