yes, all the inputs and outputs (audio & midi) communicate through the firewire port.
And you are correct. If your SOFTWARE DAW has the ability, it will see all the inputs on the interface. MC only sees 2 of them at a time. They are all available in MC but MC limits you to 2 at a time. X3 will allow them all at the same time.
The way they claim the inputs and outputs is a bit deceptive.
Yes you have the inputs they claim, but not all in a row....you have 2 on the front XLR or 1/4", you have 2 RCA on the back and apparently 2 more using the digital input from something that gives you a digital output. So you have the 6 inputs but they are in 3 different formats. You have 4 outputs on the back and the headphone out which they include in their output count as 2 more outputs. (stereo)
Variety of I/O Options Record from a variety of sources through the plethora of input and output connectors on the FA-66: 2 XLR/TRS combo inputs with phantom power, Hi-Z (Guitar) switch on input 2, stereo RCA inputs, S/PDIF optical I/O, four individual analog outputs, 1/4" stereo headphone out, and MIDI I/O.
My saffire is similar. With only 2 inputs and I do believe there is a digital input as well.... which I never used. And with 8 outputs on the back not counting the 2 headphone jacks on the front..... the outputs default as pairs... so I have 4 pairs on the back. One to my studio monitors, one to the headphone amp, another to the stereo system, and I use one of the last pair for the sub. The interface I have is actually designed to allow surround sound mixing for video game music and such things as film scoring. By sending tracks to the outputs directly, this can be accomplished, however, for me, stereo works just fine....