Setup of the USB interface with the FTDX3000 is very simple but it can seem confusing. It is only confusing because people may not be familiar with the idea of a Virtual COM Port, which only exists inside the USB connection between the FTDX3000 and the PC.
Yeasu has done a nice job of implementing the USB interface. It is explained in their USB Driver Instructions. When you install the driver it creates 2 COM Ports. One is called “Enhanced” and is used for the normal interface for CAT communications with your PC applications. The other “Standard” Port provides an Application Interface for CW keying, PTT, and FSK keying. You can see these COM Ports in the Device Manager and tweak their settings. Here is what mine looks like after installation:
I use COM6 for the CAT interface and COM5 for CW, PTT, or FSK keying. I use N1MM as my main PC Application, and use the MMTTY RTTY software which is called from N1MM. MMTTY has the ability to interface to the Virtual COM Port using something they call EXTFSK for specifying where to get the FSK binary keying signal.