One of my previous blog posts that is about recreating Atari XL/XE floppy disks describes a SIO2USB interface inside my Atari 65XE. The advantage of it is that it includes a switch that lets you toggle between the USB connection and the SIO port. This way you can easily switch between a real and virtual floppy disk that can be mounted with AspeQt software and copy real floppy disks to disks images and the other way around.
I have opened up my Atari 65XE to see how it was wired up. The connections are just as described on the AtariAge forums the only difference is the addition of a Triple Pole Double Throw (3PDT) switch, which is able to re- and disconnect the FTPD USB interface board from the Atari SIO port. Only the brown ground wire is not switchable and always connected to the FTDI board.