If I understand properly, you've got a phone like mine that allows you to connect the USB port of a PC to the phone.
Normally, the data channel itself would be set up using tcp/ip. In that case, actual messaging would be done by providing suitable client and server apps on the respective devices.
That's exactly how the latest version of Microsoft ActiveSync works, in fact. An open-source equivalent is syncE.
For me the hard part is getting the phone and the computer to configure network interface devices on the phone and the desktop PC, especially on the phone side, where there are fewer tools for configuration and for problem diagnosis.
An IDE is no substitute for an Intelligent Developer.