Hmmmm. If you're talking about saving all 16 tracks as 16 tracks, then this is not a "mixdown". A mixdown means going from 16 down to a 2-track stereo master.
So, if you want to save 16 tracks as 16 on a CD, then do a save program via the SETUP menu and use the BACK-UP -- FDMS-3 option. This is the Fostex proprietary system that saves all of the parameters you have set in the program -- EQ, effects, pans, fader positions...
To set and save parameters in a program, after you have things set the way you want, you then want to hit the SCENE-STORE key. (P.17, #14) You can enter this initial mix as is, then when you backup your 16 tracks via the CD, all settings will be on the CD. When you load from the CD back onto the VF160, all settings will be remembered by the VF160.
By the way, if you name your programs, unless you're running out of program space, just leave them on the VF160, with SCENE-STORE and each time you restart the machine you'll be all set. Using the SCENE-RECALL key (p.17, #13) it will recall all the settings, though you must go into the SETUP mode to activate fader recall (p.138). Hit the FADER ADJUST key (p.19, #52--p.21) and the display will show you where your faders were when you saved the settings on SCENE-STORE. This is great for going back to a mix to make tweaks here and there. When you're happy, then hit SCENE-STORE again and either save as initial mix, or as another mix.
Personally, I leave all my programs on the VF and only back-up a mix on CD when it's all done. Even then I still leave it on the VF as well.