With the latest 3D connexion drivers open the properties panel. You can add applications and configure to emulate the mouse or press keys with the 3Dconnexion mouse. Quite likely, Windows is like OS X, and simply adding a new application, the minecraft app to the panel will not work because this application isn't actually the one that runs, instead javac is running. If javac is in a system folder you won't have permissions to select it through the panel. The simplest solution is to instead emulate mouse and keyboard with "Any Application" selected. The only time this would be a problem is if you have several other 3D applications that also cannot be added to the list. Otherwise, you can just add those to override what you've setup for minecraft.
It will take some tweaking of thresholds to get things close to acceptable. After trying it for a while, my preference was to go back to using keyboard and mouse.
