Ah, now I see what you're asking; does it save your input levels? Nope. You'll find that when you load a song, your last input settings will be saved, but only to the extent of input selection, effects patch and any of the loop effects. Input level and trim settings are left to you to recall.
As the fader settings go, I was pretty confused by the manual's info for quite a while, but once I dug in to it I discovered that it's a very simple funciton. Press "utility"; right arrow over to the "scene" icon; press "enter"; cursor over to "save"; press "enter"--you just saved the fader levels of the current mix. Now when you load the song you can recall the saved scene and the fader levels will return to where you saved them. The faders themselves aren't motorized, so they'll stay put, but their value will change (make sense?).
Think of it this way: you mixdown a song and like the way it's sounding so you want to keep it that way without having to dial the faders in every time you load the song--save the scene. Then you mix a different tune (new fader postions). After that, you decide you want to listen to your previously mixed song without having to touch the faders--load it and go to "scene", use "call". Presto--it sounds just like before.
I'm probably confusing you at this point; just throw down some tracks, use the scene function, move the faders around then recall the scene--that will explain things best.