These topics are only loosely related and is slightly off-topic to Chris's original question.
If you are using
USB-A as two digital inputs, there is no emulation mode, the USB controller for that port is disabled and the wires normally used for USB are used for switch inputs.
USB connections have two entities, a host, like a PC or console, and a device, like a mouse or game controller. The host is in control of the connection.
The USB-B port is always a device, never a host. The USB-A port is more flexible.
The USB-A port hardware mode must be set at power up in the prefs.csv file and cannot be changed after it is initialized.
When the USB-A port is used as a device to another host, it is essentially the same as a second USB-B port.
By default (emulation mode 0), it emulates a composite device made up of a PS3 controller, mouse, keyboard and flash drive.
When USB-A is set up to work as a device, the user can switch which host the quadstick connects to by using a preference setting in a configuration file.
This is all covered in the manual.