Since you have source code, I don't think you should Wine for the device access part at all. I would recommend to split the USB interfacing code in a dll e.g. myusb.dll. Using winelib (read about winelib, winegcc in the documentation and in other places) you can build a myusb.dll.so which exports the same functions. Inside that winelib dll you can use BOTH win32 and Linux code. In this case I would just use pure Linux code to directly open your usb device and not use any win32 code. Your win32 app can just stay a win32 app but when it is loaded using wine it can pick up myusb.dll.so transparently and then use Linux usb calls. Then you can also directly access /dev/sda (or whatever the device is; probably you want to hook it up to libusb or /proc or /sys to figure out which device you need) and don't have to mount it.
